Skip to content

Instantly share code, notes, and snippets.

@athos

athos/cloverage_result.txt Secret

Created February 27, 2024 05:52
Show Gist options
  • Save athos/7a707012cacd16850951a98b5a44755a to your computer and use it in GitHub Desktop.
Save athos/7a707012cacd16850951a98b5a44755a to your computer and use it in GitHub Desktop.
Download ZIP
Raw
cloverage_result.txt
Loading namespaces: (cljam.io.protocols cljam.util.region cljam.io.util.bgzf cljam.util cljam.util.chromosome cljam.io.bed cljam.io.util.byte-buffer cljam.io.fasta.util cljam.io.util.chunk cljam.io.sam.util.refs cljam.io.sam.common cljam.io.sam.util.header cljam.io.sam.util.cigar cljam.io.util.bin cljam.io.sam.util.option cljam.io.sam.util cljam.io.sam.reader cljam.io.twobit.reader cljam.io.util.lsb.data-io cljam.io.util.lsb.io-stream cljam.io.vcf.util cljam.io.vcf.reader cljam.io.csi cljam.io.bcf.reader cljam.io.fasta.writer cljam.common cljam.io.sam.util.sequence cljam.io.bam-index.common cljam.io.bam.common cljam.io.sam.util.quality cljam.io.bam.encoder cljam.io.bam.decoder cljam.io.bam-index.writer cljam.io.bam.writer cljam.io.bigwig cljam.io.vcf.writer cljam.io.wig cljam.io.fasta-index.writer cljam.io.util.bgzf.gzi cljam.io.fasta-index.reader cljam.io.fasta-index.core cljam.io.fasta.reader cljam.io.twobit.writer cljam.io.bam-index.reader cljam.io.bam-index.core cljam.io.bam.reader cljam.io.bcf.writer cljam.io.sam.writer cljam.io.fastq cljam.io.bam-index cljam.io.bam.core cljam.io.util cljam.io.sam cljam.algo.level cljam.io.sam.util.flag cljam.algo.dedupe cljam.io.dict.writer cljam.io.cram.itf8 cljam.io.fasta.core cljam.io.sequence cljam.io.vcf.util.normalize cljam.io.dict.core cljam.io.tabix cljam.io.cram.codecs.rans4x8 cljam.io.util.lsb cljam.algo.dict cljam.io.pileup cljam.algo.pileup cljam.algo.normal cljam.util.sequence cljam.algo.convert cljam.algo.depth cljam.algo.bam-indexer cljam.algo.sorter cljam.algo.fasta-indexer cljam.tools.cli cljam.tools.main cljam.io.vcf cljam.io.vcf.util.validator cljam.io.vcf.util.check cljam.io.gff cljam.algo.vcf-indexer cljam.io.sam.util.validator cljam.util.intervals cljam.util.whole-genome)
Test namespaces: (cljam.algo.bam-indexer-test cljam.algo.convert-test cljam.algo.dedupe-test cljam.algo.depth-test cljam.algo.dict-test cljam.algo.fasta-indexer-test cljam.algo.normal-test cljam.algo.pileup-test cljam.algo.sorter-test cljam.algo.vcf-indexer-test cljam.io.bam.decoder-test cljam.io.bam.encoder-test cljam.io.bam-index.writer-test cljam.io.bam-index-test cljam.io.bam-test cljam.io.bcf.reader-test cljam.io.bcf.writer-test cljam.io.bed-test cljam.io.bigwig-test cljam.io.cram.codecs.rans4x8-test cljam.io.cram.itf8-test cljam.io.csi-test cljam.io.fasta.core-test cljam.io.fastq-test cljam.io.gff-test cljam.io.pileup-test cljam.io.sam.util.cigar-test cljam.io.sam.util.flag-test cljam.io.sam.util.header-test cljam.io.sam.util.option-test cljam.io.sam.util.refs-test cljam.io.sam.util.sequence-test cljam.io.sam.util.validator-test cljam.io.sam-test cljam.io.sequence-test cljam.io.tabix-test cljam.io.util.bgzf.gzi-test cljam.io.util.bin-test cljam.io.util.byte-buffer-test cljam.io.util.lsb.data-io-test cljam.io.util.lsb.io-stream-test cljam.io.util.lsb-test cljam.io.util-test cljam.io.vcf.reader-test cljam.io.vcf.util.check-test cljam.io.vcf.util.normalize-test cljam.io.vcf.util.validator-test cljam.io.vcf.util-test cljam.io.vcf.writer-test cljam.io.vcf-test cljam.io.wig-test cljam.test-common cljam.tools.cli-test cljam.util.chromosome-test cljam.util.intervals-test cljam.util.region-test cljam.util.sequence-test cljam.util.whole-genome-test cljam.util-test)
Instrumented cljam.io.protocols
Instrumented cljam.util.region
Instrumented cljam.io.util.bgzf
Instrumented cljam.util
Instrumented cljam.util.chromosome
Instrumented cljam.io.bed
Instrumented cljam.io.util.byte-buffer
Instrumented cljam.io.fasta.util
Instrumented cljam.io.util.chunk
Instrumented cljam.io.sam.util.refs
Instrumented cljam.io.sam.common
Instrumented cljam.io.sam.util.header
Instrumented cljam.io.sam.util.cigar
Instrumented cljam.io.util.bin
Instrumented cljam.io.sam.util.option
Instrumented cljam.io.sam.util
Instrumented cljam.io.sam.reader
Instrumented cljam.io.twobit.reader
Instrumented cljam.io.util.lsb.data-io
Instrumented cljam.io.util.lsb.io-stream
Instrumented cljam.io.vcf.util
Instrumented cljam.io.vcf.reader
Instrumented cljam.io.csi
Instrumented cljam.io.bcf.reader
Instrumented cljam.io.fasta.writer
Instrumented cljam.common
Instrumented cljam.io.sam.util.sequence
Instrumented cljam.io.bam-index.common
Instrumented cljam.io.bam.common
Instrumented cljam.io.sam.util.quality
Instrumented cljam.io.bam.encoder
Instrumented cljam.io.bam.decoder
Instrumented cljam.io.bam-index.writer
Instrumented cljam.io.bam.writer
Instrumented cljam.io.bigwig
Instrumented cljam.io.vcf.writer
Instrumented cljam.io.wig
Instrumented cljam.io.fasta-index.writer
Instrumented cljam.io.util.bgzf.gzi
Instrumented cljam.io.fasta-index.reader
Instrumented cljam.io.fasta-index.core
Instrumented cljam.io.fasta.reader
Instrumented cljam.io.twobit.writer
Instrumented cljam.io.bam-index.reader
Instrumented cljam.io.bam-index.core
Instrumented cljam.io.bam.reader
Instrumented cljam.io.bcf.writer
Instrumented cljam.io.sam.writer
Instrumented cljam.io.fastq
Instrumented cljam.io.bam-index
Instrumented cljam.io.bam.core
Instrumented cljam.io.util
Instrumented cljam.io.sam
Instrumented cljam.algo.level
Instrumented cljam.io.sam.util.flag
Instrumented cljam.algo.dedupe
Instrumented cljam.io.dict.writer
Instrumented cljam.io.cram.itf8
Instrumented cljam.io.fasta.core
Instrumented cljam.io.sequence
Instrumented cljam.io.vcf.util.normalize
Instrumented cljam.io.dict.core
Instrumented cljam.io.tabix
Instrumented cljam.io.cram.codecs.rans4x8
Instrumented cljam.io.util.lsb
Instrumented cljam.algo.dict
Instrumented cljam.io.pileup
Instrumented cljam.algo.pileup
Instrumented cljam.algo.normal
Instrumented cljam.util.sequence
Instrumented cljam.algo.convert
Instrumented cljam.algo.depth
Instrumented cljam.algo.bam-indexer
Instrumented cljam.algo.sorter
Instrumented cljam.algo.fasta-indexer
Instrumented cljam.tools.cli
Instrumented cljam.tools.main
Instrumented cljam.io.vcf
Instrumented cljam.io.vcf.util.validator
Instrumented cljam.io.vcf.util.check
Instrumented cljam.io.gff
Instrumented cljam.algo.vcf-indexer
Instrumented cljam.io.sam.util.validator
Instrumented cljam.util.intervals
Instrumented cljam.util.whole-genome
Instrumented 85 namespaces in 5.6 seconds.
Testing cljam.algo.bam-indexer-test
Testing cljam.algo.convert-test
Testing cljam.algo.dedupe-test
Testing cljam.algo.depth-test
Testing cljam.algo.dict-test
Testing cljam.algo.fasta-indexer-test
Testing cljam.algo.normal-test
Testing cljam.algo.pileup-test
Testing cljam.algo.sorter-test
Testing cljam.algo.vcf-indexer-test
FAIL in (about-vcf-skipped-chr-order) (vcf_indexer_test.clj:225)
expected: (= [{37449 [{:beg 117, :end 136}], 299594 [{:beg 117, :end 136} {:beg 1, :end 0}]} {37449 [{:beg 136, :end 10682368}], 299594 [{:beg 136, :end 10682368} {:beg 1, :end 0}]}] (-> (unrecord (.bidx csi)) (assoc-in [1 37449 0 :end] 10682368) (assoc-in [1 299594 0 :end] 10682368)) (unrecord (.bidx computed)))
actual: (not (= [{37449 [{:beg 117, :end 136}], 299594 [{:beg 117, :end 136} {:beg 1, :end 0}]} {37449 [{:beg 136, :end 10682368}], 299594 [{:beg 136, :end 10682368} {:beg 1, :end 0}]}] [{37449 [{:beg 117, :end 136}], 299594 [{:beg 117, :end 136} {:beg 1, :end 0}]} {37449 [{:beg 136, :end 10682368}], 299594 [{:beg 136, :end 10682368} {:beg 1, :end 0}]}] [{299594 [{:beg 117, :end 136} {:beg 1, :end 0}], 37448 [{:beg 117, :end 136}]} {299594 [{:beg 136, :end 10682368} {:beg 1, :end 0}], 37448 [{:beg 136, :end 10682368}]}]))
FAIL in (about-vcf-skipped-chr-order) (vcf_indexer_test.clj:235)
expected: (= [{1 117} {1 136}] (.loffset csi) (.loffset computed))
actual: (not (= [{1 117} {1 136}] [{1 117} {1 136}] [{4294836225 0} {4294836225 0}]))
FAIL in (about-vcf-indexer) (vcf_indexer_test.clj:61)
vcf
expected: (= [{1 3904} {32769 3973} {114704385 4031} {1 4783}] (.loffset csi) (.loffset computed))
actual: (not (= [{1 3904} {32769 3973} {114704385 4031} {1 4783}] [{1 3904} {32769 3973} {114704385 4031} {1 4783}] [{4294836225 0} {4294836225 0} {4294836225 0} {4294836225 0}]))
FAIL in (about-vcf-indexer) (vcf_indexer_test.clj:67)
vcf
expected: (= [{37449 [{:beg 3904, :end 3973}], 299594 [{:beg 3904, :end 3973} {:beg 1, :end 0}]} {37451 [{:beg 3973, :end 4031}], 299594 [{:beg 3973, :end 4031} {:beg 1, :end 0}]} {44450 [{:beg 4031, :end 4783}], 299594 [{:beg 4031, :end 4783} {:beg 1, :end 0}]} {37449 [{:beg 4783, :end 106168320}], 299594 [{:beg 4783, :end 106168320} {:beg 1, :end 0}]}] (-> (unrecord (.bidx csi)) (assoc-in [3 37449 0 :end] 106168320) (assoc-in [3 299594 0 :end] 106168320)) (unrecord (.bidx computed)))
actual: (not (= [{37449 [{:beg 3904, :end 3973}], 299594 [{:beg 3904, :end 3973} {:beg 1, :end 0}]} {37451 [{:beg 3973, :end 4031}], 299594 [{:beg 3973, :end 4031} {:beg 1, :end 0}]} {44450 [{:beg 4031, :end 4783}], 299594 [{:beg 4031, :end 4783} {:beg 1, :end 0}]} {37449 [{:beg 4783, :end 106168320}], 299594 [{:beg 4783, :end 106168320} {:beg 1, :end 0}]}] [{37449 [{:beg 3904, :end 3973}], 299594 [{:beg 3904, :end 3973} {:beg 1, :end 0}]} {299594 [{:beg 3973, :end 4031} {:beg 1, :end 0}], 37451 [{:beg 3973, :end 4031}]} {44450 [{:beg 4031, :end 4783}], 299594 [{:beg 4031, :end 4783} {:beg 1, :end 0}]} {37449 [{:beg 4783, :end 106168320}], 299594 [{:beg 4783, :end 106168320} {:beg 1, :end 0}]}] [{299594 [{:beg 3904, :end 3973} {:beg 1, :end 0}], 37448 [{:beg 3904, :end 3973}]} {299594 [{:beg 3973, :end 4031} {:beg 1, :end 0}], 37448 [{:beg 3973, :end 4031}]} {299594 [{:beg 4031, :end 4783} {:beg 1, :end 0}], 37448 [{:beg 4031, :end 4783}]} {299594 [{:beg 4783, :end 106168320} {:beg 1, :end 0}], 37448 [{:beg 4783, :end 106168320}]}]))
FAIL in (about-vcf-indexer) (vcf_indexer_test.clj:109)
vcf
expected: (= (.loffset computed) [{1 3904} {1 3973} {114556929 4031} {1 4783}])
actual: (not (= [{8587837441 0} {8587837441 0} {8587837441 0} {8587837441 0}] [{1 3904} {1 3973} {114556929 4031} {1 4783}]))
FAIL in (about-vcf-indexer) (vcf_indexer_test.clj:114)
vcf
expected: (= [{4681 [{:beg 3904, :end 3973}], 37450 [{:beg 3904, :end 3973} {:beg 1, :end 0}]} {4681 [{:beg 3973, :end 4031}], 37450 [{:beg 3973, :end 4031} {:beg 1, :end 0}]} {5118 [{:beg 4031, :end 4783}], 37450 [{:beg 4031, :end 4783} {:beg 1, :end 0}]} {4681 [{:beg 4783, :end 106168320}], 37450 [{:beg 4783, :end 106168320} {:beg 1, :end 0}]}] (unrecord (.bidx computed)))
actual: (not (= [{4681 [{:beg 3904, :end 3973}], 37450 [{:beg 3904, :end 3973} {:beg 1, :end 0}]} {4681 [{:beg 3973, :end 4031}], 37450 [{:beg 3973, :end 4031} {:beg 1, :end 0}]} {5118 [{:beg 4031, :end 4783}], 37450 [{:beg 4031, :end 4783} {:beg 1, :end 0}]} {4681 [{:beg 4783, :end 106168320}], 37450 [{:beg 4783, :end 106168320} {:beg 1, :end 0}]}] [{37450 [{:beg 3904, :end 3973} {:beg 1, :end 0}], 4680 [{:beg 3904, :end 3973}]} {37450 [{:beg 3973, :end 4031} {:beg 1, :end 0}], 4680 [{:beg 3973, :end 4031}]} {37450 [{:beg 4031, :end 4783} {:beg 1, :end 0}], 4680 [{:beg 4031, :end 4783}]} {37450 [{:beg 4783, :end 106168320} {:beg 1, :end 0}], 4680 [{:beg 4783, :end 106168320}]}]))
FAIL in (about-vcf-changed-chr-order-field-less) (vcf_indexer_test.clj:201)
expected: (= [{4681 [{:beg 1597, :end 1761}], 4685 [{:beg 1761, :end 2046}], 37450 [{:beg 1597, :end 2046} {:beg 6, :end 0}]} {4681 [{:beg 2046, :end 2155}], 37450 [{:beg 2046, :end 2155} {:beg 2, :end 0}]} {4681 [{:beg 2155, :end 70057984}], 37450 [{:beg 2155, :end 70057984} {:beg 4, :end 0}]}] (unrecord (.bidx csi)))
actual: (not (= [{4681 [{:beg 1597, :end 1761}], 4685 [{:beg 1761, :end 2046}], 37450 [{:beg 1597, :end 2046} {:beg 6, :end 0}]} {4681 [{:beg 2046, :end 2155}], 37450 [{:beg 2046, :end 2155} {:beg 2, :end 0}]} {4681 [{:beg 2155, :end 70057984}], 37450 [{:beg 2155, :end 70057984} {:beg 4, :end 0}]}] [{37450 [{:beg 1597, :end 2046} {:beg 6, :end 0}], 4680 [{:beg 1597, :end 2046}]} {37450 [{:beg 2046, :end 2155} {:beg 2, :end 0}], 4680 [{:beg 2046, :end 2155}]} {37450 [{:beg 2155, :end 70057984} {:beg 4, :end 0}], 4680 [{:beg 2155, :end 70057984}]}]))
FAIL in (about-vcf-changed-chr-order-field-less) (vcf_indexer_test.clj:209)
expected: (= [{1 1597, 1048577 1761} {1 2046} {1 2155}] (.loffset csi))
actual: (not (= [{1 1597, 1048577 1761} {1 2046} {1 2155}] [{8587837441 0} {8587837441 0} {8587837441 0}]))
FAIL in (about-vcf-changed-chr-order) (vcf_indexer_test.clj:152)
vcf
expected: (= [{4681 [{:beg 2096, :end 2205}], 37450 [{:beg 2096, :end 2205} {:beg 2, :end 0}]} {4681 [{:beg 1647, :end 1811}], 4685 [{:beg 1811, :end 2096}], 37450 [{:beg 1647, :end 2096} {:beg 6, :end 0}]} {4681 [{:beg 2205, :end 70975488}], 37450 [{:beg 2205, :end 70975488} {:beg 4, :end 0}]}] (unrecord (.bidx csi)))
actual: (not (= [{4681 [{:beg 2096, :end 2205}], 37450 [{:beg 2096, :end 2205} {:beg 2, :end 0}]} {4681 [{:beg 1647, :end 1811}], 4685 [{:beg 1811, :end 2096}], 37450 [{:beg 1647, :end 2096} {:beg 6, :end 0}]} {4681 [{:beg 2205, :end 70975488}], 37450 [{:beg 2205, :end 70975488} {:beg 4, :end 0}]}] [{37450 [{:beg 2096, :end 2205} {:beg 2, :end 0}], 4680 [{:beg 2096, :end 2205}]} {37450 [{:beg 1647, :end 2096} {:beg 6, :end 0}], 4680 [{:beg 1647, :end 2096}]} {37450 [{:beg 2205, :end 70975488} {:beg 4, :end 0}], 4680 [{:beg 2205, :end 70975488}]}]))
FAIL in (about-vcf-changed-chr-order) (vcf_indexer_test.clj:160)
vcf
expected: (= (.loffset csi) [{1 2096} {1 1647, 1048577 1811} {1 2205}])
actual: (not (= [{8587837441 0} {8587837441 0} {8587837441 0}] [{1 2096} {1 1647, 1048577 1811} {1 2205}]))
FAIL in (about-vcf-changed-chr-order) (vcf_indexer_test.clj:177)
bcf
expected: (= [{37449 [{:beg 2275, :end 2387}], 299594 [{:beg 2275, :end 2387} {:beg 2, :end 0}]} {37449 [{:beg 1862, :end 1940}], 37450 [{:beg 1940, :end 2009}], 37516 [{:beg 2009, :end 2089}], 37524 [{:beg 2089, :end 2275}], 299594 [{:beg 1862, :end 2275} {:beg 6, :end 0}]} {37449 [{:beg 2387, :end 79953920}], 299594 [{:beg 2387, :end 79953920} {:beg 4, :end 0}]}] (unrecord (.bidx csi)) (unrecord (.bidx computed)))
actual: (not (= [{37449 [{:beg 2275, :end 2387}], 299594 [{:beg 2275, :end 2387} {:beg 2, :end 0}]} {37449 [{:beg 1862, :end 1940}], 37450 [{:beg 1940, :end 2009}], 37516 [{:beg 2009, :end 2089}], 37524 [{:beg 2089, :end 2275}], 299594 [{:beg 1862, :end 2275} {:beg 6, :end 0}]} {37449 [{:beg 2387, :end 79953920}], 299594 [{:beg 2387, :end 79953920} {:beg 4, :end 0}]}] [{37449 [{:beg 2275, :end 2387}], 299594 [{:beg 2275, :end 2387} {:beg 2, :end 0}]} {37449 [{:beg 1862, :end 1940}], 37450 [{:beg 1940, :end 2009}], 299594 [{:beg 1862, :end 2275} {:beg 6, :end 0}], 37516 [{:beg 2009, :end 2089}], 37524 [{:beg 2089, :end 2275}]} {37449 [{:beg 2387, :end 79953920}], 299594 [{:beg 2387, :end 79953920} {:beg 4, :end 0}]}] [{299594 [{:beg 2275, :end 2387} {:beg 2, :end 0}], 1125899906880072 [{:beg 2275, :end 2387}]} {299594 [{:beg 1862, :end 2275} {:beg 6, :end 0}], 1125899906880072 [{:beg 1862, :end 2275}]} {299594 [{:beg 2387, :end 79953920} {:beg 4, :end 0}], 1125899906880072 [{:beg 2387, :end 79953920}]}]))
FAIL in (csi-comparison-test) (vcf_indexer_test.clj:272)
vcf
expected: (= (update (.bidx csi) 0 dissoc 75 299594) (update (.bidx computed) 0 dissoc 75 299594))
actual: (not (= [{4721 [#cljam.io.util.chunk.Chunk{:beg 459627198894, :end 459627215303}], 73 [#cljam.io.util.chunk.Chunk{:beg 36818987239, :end 71637224204} #cljam.io.util.chunk.Chunk{:beg 301574199307, :end 331807471164} #cljam.io.util.chunk.Chunk{:beg 340358873545, :end 370604269560} #cljam.io.util.chunk.Chunk{:beg 379870473707, :end 459627198894}], 4681 [#cljam.io.util.chunk.Chunk{:beg 703, :end 2540291630} #cljam.io.util.chunk.Chunk{:beg 247995949343, :end 251291706540} #cljam.io.util.chunk.Chunk{:beg 268577928249, :end 269052081557}], 4682 [#cljam.io.util.chunk.Chunk{:beg 331807471164, :end 331807520363} #cljam.io.util.chunk.Chunk{:beg 370604269560, :end 370604285993}], 585 [#cljam.io.util.chunk.Chunk{:beg 2540291630, :end 36818987239} #cljam.io.util.chunk.Chunk{:beg 251291706540, :end 268577928249} #cljam.io.util.chunk.Chunk{:beg 269052081557, :end 301574199307} #cljam.io.util.chunk.Chunk{:beg 331807520363, :end 340358873545} #cljam.io.util.chunk.Chunk{:beg 370604285993, :end 379870473707}], 9 [#cljam.io.util.chunk.Chunk{:beg 71637224204, :end 247995949343}]}] [{1125899906880072 [#cljam.io.util.chunk.Chunk{:beg 703, :end 536650514432}]}]))
ERROR in (csi-comparison-test) (RT.java:1473)
vcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742$fn__22807.invoke (vcf_indexer_test.clj:278)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742.invoke (vcf_indexer_test.clj:277)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:257)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
vcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742$fn__22807.invoke (vcf_indexer_test.clj:278)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742.invoke (vcf_indexer_test.clj:277)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:257)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
vcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742$fn__22807.invoke (vcf_indexer_test.clj:278)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742.invoke (vcf_indexer_test.clj:277)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:257)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
vcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742$fn__22807.invoke (vcf_indexer_test.clj:278)
cljam.algo.vcf_indexer_test$fn__22741$fn__22742.invoke (vcf_indexer_test.clj:277)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:257)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
FAIL in (csi-comparison-test) (vcf_indexer_test.clj:293)
bcf
expected: (= (.bidx csi) (.bidx computed))
actual: (not (= [{4721 [#cljam.io.util.chunk.Chunk{:beg 459678777304, :end 459678793727}], 73 [#cljam.io.util.chunk.Chunk{:beg 36823575264, :end 71639125297} #cljam.io.util.chunk.Chunk{:beg 301573479531, :end 331816450750} #cljam.io.util.chunk.Chunk{:beg 340373751471, :end 370619737344} #cljam.io.util.chunk.Chunk{:beg 379894002577, :end 459678777304}], 4681 [#cljam.io.util.chunk.Chunk{:beg 858, :end 2544748363} #cljam.io.util.chunk.Chunk{:beg 247999488858, :end 251289282378} #cljam.io.util.chunk.Chunk{:beg 268586972995, :end 269046249694}], 4682 [#cljam.io.util.chunk.Chunk{:beg 331816450750, :end 331816499981} #cljam.io.util.chunk.Chunk{:beg 370619737344, :end 370619753804}], 585 [#cljam.io.util.chunk.Chunk{:beg 2544748363, :end 36823575264} #cljam.io.util.chunk.Chunk{:beg 251289282378, :end 268586972995} #cljam.io.util.chunk.Chunk{:beg 269046249694, :end 301573479531} #cljam.io.util.chunk.Chunk{:beg 331816499981, :end 340373751471} #cljam.io.util.chunk.Chunk{:beg 370619753804, :end 379894002577}], 299594 [#cljam.io.util.chunk.Chunk{:beg 858, :end 536746065920} #cljam.io.util.chunk.Chunk{:beg 84, :end 0}], 75 [#cljam.io.util.chunk.Chunk{:beg 459678793727, :end 536746065920}], 9 [#cljam.io.util.chunk.Chunk{:beg 71639125297, :end 247999488858}]}] [{299594 [#cljam.io.util.chunk.Chunk{:beg 858, :end 536746065920} #cljam.io.util.chunk.Chunk{:beg 84, :end 0}], 1125899906880072 [#cljam.io.util.chunk.Chunk{:beg 858, :end 536746065920}]}]))
ERROR in (csi-comparison-test) (RT.java:1473)
bcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22882.invoke (vcf_indexer_test.clj:298)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:297)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
bcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22882.invoke (vcf_indexer_test.clj:298)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:297)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
bcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22882.invoke (vcf_indexer_test.clj:298)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:297)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
ERROR in (csi-comparison-test) (RT.java:1473)
bcf
expected: (or (= offset (get l-comp beg)) (check-loffset file-offsets file-offset-index beg (get l-comp beg)))
actual: java.lang.NullPointerException: Cannot invoke "java.lang.Character.charValue()" because "x" is null
at clojure.lang.RT.uncheckedIntCast (RT.java:1473)
cljam.algo.vcf_indexer_test$check_loffset.invokeStatic (vcf_indexer_test.clj:44)
cljam.algo.vcf_indexer_test$check_loffset.invoke (vcf_indexer_test.clj:39)
cljam.algo.vcf_indexer_test$fn__22741$fn__22882.invoke (vcf_indexer_test.clj:298)
cljam.algo.vcf_indexer_test$fn__22741.invokeStatic (vcf_indexer_test.clj:297)
cljam.algo.vcf_indexer_test/fn (vcf_indexer_test.clj:256)
clojure.test$test_var$fn__9856.invoke (test.clj:717)
clojure.test$test_var.invokeStatic (test.clj:717)
clojure.test$test_var.invoke (test.clj:708)
clojure.test$test_vars$fn__9882$fn__9887.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars$fn__9882.invoke (test.clj:735)
clojure.test$default_fixture.invokeStatic (test.clj:687)
clojure.test$default_fixture.invoke (test.clj:683)
clojure.test$test_vars.invokeStatic (test.clj:731)
clojure.test$test_all_vars.invokeStatic (test.clj:737)
clojure.test$test_ns.invokeStatic (test.clj:758)
clojure.test$test_ns.invoke (test.clj:743)
clojure.core$map$fn__5935.invoke (core.clj:2772)
clojure.lang.LazySeq.sval (LazySeq.java:42)
clojure.lang.LazySeq.seq (LazySeq.java:51)
clojure.lang.Cons.next (Cons.java:39)
clojure.lang.RT.next (RT.java:713)
clojure.core$next__5451.invokeStatic (core.clj:64)
clojure.core$reduce1.invokeStatic (core.clj:946)
clojure.core$reduce1.invokeStatic (core.clj:936)
clojure.core$merge_with.invokeStatic (core.clj:3076)
clojure.core$merge_with.doInvoke (core.clj:3068)
clojure.lang.RestFn.applyTo (RestFn.java:139)
clojure.core$apply.invokeStatic (core.clj:669)
clojure.test$run_tests.invokeStatic (test.clj:768)
clojure.test$run_tests.doInvoke (test.clj:768)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$apply.invoke (core.clj:662)
cloverage.coverage$eval4934$fn__4936$fn__4938$run_tests__4939.invoke (coverage.clj:213)
cloverage.coverage$eval4934$fn__4936$fn__4938.invoke (coverage.clj:219)
cloverage.coverage$run_tests$fn__4967.invoke (coverage.clj:257)
cloverage.coverage$form_for_suppressing_unselected_tests.invokeStatic (coverage.clj:54)
cloverage.coverage$form_for_suppressing_unselected_tests.invoke (coverage.clj:32)
cloverage.coverage$run_tests.invokeStatic (coverage.clj:255)
cloverage.coverage$run_tests.invoke (coverage.clj:245)
cloverage.coverage$run_main.invokeStatic (coverage.clj:307)
cloverage.coverage$run_main.invoke (coverage.clj:299)
cloverage.coverage$run_project.invokeStatic (coverage.clj:323)
cloverage.coverage$run_project.doInvoke (coverage.clj:319)
clojure.lang.RestFn.invoke (RestFn.java:410)
user$eval4987.invokeStatic (form-init8055630609029633083.clj:1)
user$eval4987.invoke (form-init8055630609029633083.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7194)
clojure.lang.Compiler.eval (Compiler.java:7184)
clojure.lang.Compiler.load (Compiler.java:7653)
clojure.lang.Compiler.loadFile (Compiler.java:7591)
clojure.main$load_script.invokeStatic (main.clj:475)
clojure.main$init_opt.invokeStatic (main.clj:477)
clojure.main$init_opt.invoke (main.clj:477)
clojure.main$initialize.invokeStatic (main.clj:508)
clojure.main$null_opt.invokeStatic (main.clj:542)
clojure.main$null_opt.invoke (main.clj:539)
clojure.main$main.invokeStatic (main.clj:664)
clojure.main$main.doInvoke (main.clj:616)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:40)
Testing cljam.io.bam.decoder-test
Testing cljam.io.bam.encoder-test
Testing cljam.io.bam-index.writer-test
Testing cljam.io.bam-index-test
Testing cljam.io.bam-test
Testing cljam.io.bcf.reader-test
Testing cljam.io.bcf.writer-test
Testing cljam.io.bed-test
Testing cljam.io.bigwig-test
Testing cljam.io.cram.codecs.rans4x8-test
Testing cljam.io.cram.itf8-test
Testing cljam.io.csi-test
Testing cljam.io.fasta.core-test
Testing cljam.io.fastq-test
Testing cljam.io.gff-test
Testing cljam.io.pileup-test
Testing cljam.io.sam.util.cigar-test
Testing cljam.io.sam.util.flag-test
Testing cljam.io.sam.util.header-test
Testing cljam.io.sam.util.option-test
Testing cljam.io.sam.util.refs-test
Testing cljam.io.sam.util.sequence-test
Testing cljam.io.sam.util.validator-test
Testing cljam.io.sam-test
FAIL in (bam-reader-with-index-test) (sam_test.clj:157)
read-alignments
expected: (= (sam/read-alignments rdr {:chr "ref2"}) (drop 6 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x1", :flag 0, :rname "ref2", :pos 1, :end 20, :mapq 30, :cigar "20M", :rnext "*", :pnext 0, :tlen 0, :seq "AGGTTTTATAAAACAAATAA", :qual "????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:160)
read-alignments
expected: (= (sam/read-alignments rdr {:chr "ref2", :start 21}) (drop 7 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:174)
read-blocks
expected: (= (map (fn* [p1__27576#] (dissoc p1__27576# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2"} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:178)
read-blocks
expected: (= (map (fn* [p1__27577#] (dissoc p1__27577# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2", :start 2} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:174)
read-blocks
expected: (= (map (fn* [p1__27576#] (dissoc p1__27576# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2"} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:178)
read-blocks
expected: (= (map (fn* [p1__27577#] (dissoc p1__27577# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2", :start 2} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:174)
read-blocks
expected: (= (map (fn* [p1__27576#] (dissoc p1__27576# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2"} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:178)
read-blocks
expected: (= (map (fn* [p1__27577#] (dissoc p1__27577# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2", :start 2} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:174)
read-blocks
expected: (= (map (fn* [p1__27576#] (dissoc p1__27576# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2"} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:178)
read-blocks
expected: (= (map (fn* [p1__27577#] (dissoc p1__27577# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2", :start 2} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:174)
read-blocks
expected: (= (map (fn* [p1__27576#] (dissoc p1__27576# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2"} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:178)
read-blocks
expected: (= (map (fn* [p1__27577#] (dissoc p1__27577# :pos :qname :rname :flag :ref-id)) (data->clj (sam/read-blocks rdr {:chr "ref2", :start 2} {:mode mode}))) (drop 6 test-sorted-bam-data))
actual: (not (= () ({:data [1 0 0 0 0 0 0 0 3 30 73 18 1 0 0 0 20 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 49 0 64 1 0 0 20 72 -120 -127 -127 17 18 17 24 17 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 1 0 0 0 3 30 73 18 1 0 0 0 21 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 50 0 80 1 0 0 68 -120 -120 24 17 17 33 17 -127 24 -128 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 5 0 0 0 3 30 73 18 3 0 0 0 26 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 51 0 -112 0 0 0 65 0 0 0 -48 0 0 0 -120 24 17 17 33 17 -127 24 -127 20 -126 -127 33 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 9 0 0 0 3 30 73 18 1 0 0 0 25 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 52 0 -112 1 0 0 33 17 -127 24 -127 20 -126 -127 33 65 66 17 32 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 11 0 0 0 3 30 73 18 1 0 0 0 24 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 53 0 -128 1 0 0 17 -127 24 -127 20 -126 -127 33 65 66 17 40 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]} {:data [1 0 0 0 13 0 0 0 3 30 73 18 1 0 0 0 23 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 120 54 0 112 1 0 0 -127 24 -127 20 -126 -127 33 65 66 17 40 16 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30]})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:191)
read-in-region
expected: (= (protocols/read-in-region rdr {:chr "ref2"}) (drop 6 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x1", :flag 0, :rname "ref2", :pos 1, :end 20, :mapq 30, :cigar "20M", :rnext "*", :pnext 0, :tlen 0, :seq "AGGTTTTATAAAACAAATAA", :qual "????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:193)
read-in-region
expected: (= (protocols/read-in-region rdr {:chr "ref2", :start 21}) (drop 7 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:198)
read-in-region
expected: (= (protocols/read-in-region rdr {:chr "ref2"} {}) (drop 6 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x1", :flag 0, :rname "ref2", :pos 1, :end 20, :mapq 30, :cigar "20M", :rnext "*", :pnext 0, :tlen 0, :seq "AGGTTTTATAAAACAAATAA", :qual "????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-index-test) (sam_test.clj:200)
read-in-region
expected: (= (protocols/read-in-region rdr {:chr "ref2", :start 21} {}) (drop 7 (:alignments test-sam-sorted-by-pos)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "x2", :flag 0, :rname "ref2", :pos 2, :end 22, :mapq 30, :cigar "21M", :rnext "*", :pnext 0, :tlen 0, :seq "GGTTTTATAAAACAAATAATT", :qual "?????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x3", :flag 0, :rname "ref2", :pos 6, :end 27, :mapq 30, :cigar "9M4I13M", :rnext "*", :pnext 0, :tlen 0, :seq "TTATAAAACAAATAATTAAGTCTACA", :qual "??????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x4", :flag 0, :rname "ref2", :pos 10, :end 34, :mapq 30, :cigar "25M", :rnext "*", :pnext 0, :tlen 0, :seq "CAAATAATTAAGTCTACAGAGCAAC", :qual "?????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x5", :flag 0, :rname "ref2", :pos 12, :end 35, :mapq 30, :cigar "24M", :rnext "*", :pnext 0, :tlen 0, :seq "AATAATTAAGTCTACAGAGCAACT", :qual "????????????????????????", :options []} #cljam.io.protocols.SAMAlignment{:qname "x6", :flag 0, :rname "ref2", :pos 14, :end 36, :mapq 30, :cigar "23M", :rnext "*", :pnext 0, :tlen 0, :seq "TAATTAAGTCTACAGAGCAACTA", :qual "???????????????????????", :options []})))
FAIL in (bam-reader-with-asterisk-seq-test) (sam_test.clj:214)
expected: (= (sam/read-alignments rdr {:chr "ref"}) (filter (fn* [p1__27688#] (= (:rname p1__27688#) "ref")) (sam/read-alignments rdr)))
actual: (not (= () (#cljam.io.protocols.SAMAlignment{:qname "r", :flag 1, :rname "ref", :pos 1, :end 76, :mapq 1, :cigar "76M", :rnext "*", :pnext 0, :tlen 0, :seq "*", :qual "*", :options ()})))
Testing cljam.io.sequence-test
Testing cljam.io.tabix-test
Testing cljam.io.util.bgzf.gzi-test
Testing cljam.io.util.bin-test
FAIL in (reg->bin-test) (bin_test.clj:182)
various min-shfits and depths
expected: (= (util-bin/reg->bin 1 1 14 6) 37449)
actual: (not (= 1125899906880072 37449))
FAIL in (reg->bin-test) (bin_test.clj:183)
various min-shfits and depths
expected: (= (util-bin/reg->bin 1 1 14 7) 299593)
actual: (not (= 1125899907142216 299593))
FAIL in (reg->bin-test) (bin_test.clj:184)
various min-shfits and depths
expected: (= (util-bin/reg->bin 1 32769 15 6) 4681)
actual: (not (= 562949953458760 4681))
FAIL in (reg->bin-test) (bin_test.clj:185)
various min-shfits and depths
expected: (= (util-bin/reg->bin 240877561 240877568 14 6) 52150)
actual: (not (= 1125899906880072 52150))
FAIL in (reg->bins-test) (bin_test.clj:127)
expected: (= [0 1 9 73 585 4681] (util-bin/reg->bins 1 (bit-shift-left 1 16) 16 5))
actual: (not (= [0 1 9 73 585 4681] [0 -8 -56 -440 -3512 -28088]))
FAIL in (reg->bins-test) (bin_test.clj:130)
expected: (= [0 1 9 73 585 4681 4682] (util-bin/reg->bins 1 (inc (bit-shift-left 1 16)) 16 5))
actual: (not (= [0 1 9 73 585 4681 4682] [0 -8 -56 -440 -3512 -28088]))
FAIL in (reg->bins-test) (bin_test.clj:139)
expected: (= [0 1 9 73 585 4681 37449] (util-bin/reg->bins 1 1 14 6))
actual: (not (= [0 1 9 73 585 4681 37449] [0 0 8 72 584 4680 37448]))
FAIL in (reg->bins-test) (bin_test.clj:141)
expected: (= [0 1 9 73 585 4681 37449 299593] (util-bin/reg->bins 1 1 14 7))
actual: (not (= [0 1 9 73 585 4681 37449 299593] [0 0 8 72 584 4680 37448 299592]))
FAIL in (reg->bins-test) (bin_test.clj:143)
expected: (= [0 1 9 73 585 4681 37449 37450] (util-bin/reg->bins 1 32769 15 6))
actual: (not (= [0 1 9 73 585 4681 37449 37450] [0 0 8 72 584 4680 37448]))
FAIL in (get-spans-returns-a-sequence-including-regions) (bin_test.clj:195)
expected: (= [[3904 3973]] (util-bin/get-spans csi* 0 1 100000))
actual: (not (= [[3904 3973]] ()))
Testing cljam.io.util.byte-buffer-test
Testing cljam.io.util.lsb.data-io-test
Testing cljam.io.util.lsb.io-stream-test
Testing cljam.io.util.lsb-test
Testing cljam.io.util-test
Testing cljam.io.vcf.reader-test
Testing cljam.io.vcf.util.check-test
Testing cljam.io.vcf.util.normalize-test
Testing cljam.io.vcf.util.validator-test
Testing cljam.io.vcf.util-test
Testing cljam.io.vcf.writer-test
Testing cljam.io.vcf-test
FAIL in (read-randomly-variants-complex-test) (vcf_test.clj:224)
expected: (= (vcf/read-variants-randomly vcf-gz-file index {}) (vcf/read-variants-randomly bcf-file index {}) (let [{:keys [chr start end], :or {start 1, end 4294967296}} index] (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= chr chr') (<= start (get info :END (dec (+ pos (count ref'))))) (>= end pos))) (vcf/read-variants vcf-file))))
actual: (not (= nil nil ({:SAMPLE01 nil, :alt nil, :SAMPLE02 nil, :ref "N", :SAMPLE03 nil, :FORMAT nil, :pos 1, :filter nil, :id "Semicolon;separated;list;of;unique;identifiers", :info nil, :qual nil, :chr "1"})))
FAIL in (read-randomly-variants-complex-test) (vcf_test.clj:224)
expected: (= (vcf/read-variants-randomly vcf-gz-file index {}) (vcf/read-variants-randomly bcf-file index {}) (let [{:keys [chr start end], :or {start 1, end 4294967296}} index] (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= chr chr') (<= start (get info :END (dec (+ pos (count ref'))))) (>= end pos))) (vcf/read-variants vcf-file))))
actual: (not (= nil nil ({:SAMPLE01 {:GT "0/0"}, :alt ["G"], :SAMPLE02 {:GT "1|0"}, :ref "A", :SAMPLE03 {:GT "0/1"}, :FORMAT (:GT), :pos 35416, :filter (:PASS), :id nil, :info {:AC (3), :AF (0.5), :END 35416}, :qual nil, :chr "2"})))
FAIL in (read-randomly-variants-complex-test) (vcf_test.clj:224)
expected: (= (vcf/read-variants-randomly vcf-gz-file index {}) (vcf/read-variants-randomly bcf-file index {}) (let [{:keys [chr start end], :or {start 1, end 4294967296}} index] (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= chr chr') (<= start (get info :END (dec (+ pos (count ref'))))) (>= end pos))) (vcf/read-variants vcf-file))))
actual: (not (= nil nil ()))
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 1, :end 16384} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 16384 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 1, :end 49153} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 49153 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 1, :end 30000} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 30000 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 49153, :end 147457} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 49153 (get info :END (dec (+ pos (count ref'))))) (>= 147457 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 32769, :end 147457} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 32769 (get info :END (dec (+ pos (count ref'))))) (>= 147457 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 49153, :end 1064952} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 49153 (get info :END (dec (+ pos (count ref'))))) (>= 1064952 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 1048577, :end 414826496} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1048577 (get info :END (dec (+ pos (count ref'))))) (>= 414826496 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 1048577, :end 414826497} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1048577 (get info :END (dec (+ pos (count ref'))))) (>= 414826497 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:417)
vcf
expected: (let [vcf1* (vcf/vcf-reader test-vcf-various-bins-gz-file) vcf2* (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly vcf1* {:chr "chr1", :start 32769, :end 414859265} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 32769 (get info :END (dec (+ pos (count ref'))))) (>= 414859265 pos))) (vcf/read-variants vcf2*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 1, :end 16384} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 1, :end 16384} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 16384 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 1, :end 49153} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 1, :end 49153} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 49153 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 1, :end 30000} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 1, :end 30000} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1 (get info :END (dec (+ pos (count ref'))))) (>= 30000 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 49153, :end 147457} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 49153, :end 147457} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 49153 (get info :END (dec (+ pos (count ref'))))) (>= 147457 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 32769, :end 147457} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 32769, :end 147457} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 32769 (get info :END (dec (+ pos (count ref'))))) (>= 147457 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 49153, :end 1064952} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 49153, :end 1064952} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 49153 (get info :END (dec (+ pos (count ref'))))) (>= 1064952 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 1048577, :end 414826496} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 1048577, :end 414826496} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1048577 (get info :END (dec (+ pos (count ref'))))) (>= 414826496 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 1048577, :end 414826497} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 1048577, :end 414826497} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 1048577 (get info :END (dec (+ pos (count ref'))))) (>= 414826497 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-test) (vcf_test.clj:439)
bcf
expected: (let [bcf1* (vcf/bcf-reader test-bcf-various-bins-file) bcf2* (vcf/bcf-reader test-bcf-various-bins-file) vcf (vcf/vcf-reader test-vcf-various-bins-gz-file)] (= (vcf/read-variants-randomly bcf2* {:chr "chr1", :start 32769, :end 414859265} {}) (vcf/read-variants-randomly vcf {:chr "chr1", :start 32769, :end 414859265} {}) (filter (fn [{chr' :chr, :keys [pos info], ref' :ref}] (and (= "chr1" chr') (<= 32769 (get info :END (dec (+ pos (count ref'))))) (>= 414859265 pos))) (vcf/read-variants bcf1*))))
actual: false
FAIL in (read-variants-randomly-with-irregular-chr-test) (vcf_test.clj:464)
expected: (= (vcf/read-variants-randomly r {:chr "chr3"} {}) (quote ({:alt ["C"], :ref "G", :pos 1, :filter nil, :id nil, :info nil, :qual nil, :chr "chr3"})))
actual: (not (= nil ({:alt ["C"], :ref "G", :pos 1, :filter nil, :id nil, :info nil, :qual nil, :chr "chr3"})))
FAIL in (read-variants-randomly-with-irregular-chr-test) (vcf_test.clj:469)
expected: (= (vcf/read-variants-randomly r {:chr "19"} {}) (quote ({:NA00001 {:GT "0|0", :HQ (10 10)}, :alt ["C"], :ref "A", :FORMAT (:GT :HQ), :NA00002 {:GT "0|0", :HQ (10 10)}, :pos 111, :filter nil, :id nil, :info nil, :qual 9.6, :NA00003 {:GT "0/1", :HQ (3 3)}, :chr "19"} {:NA00001 {:GT "0|0", :HQ (10 10)}, :alt ["G"], :ref "A", :FORMAT (:GT :HQ), :NA00002 {:GT "0|0", :HQ (10 10)}, :pos 112, :filter nil, :id nil, :info nil, :qual 10.0, :NA00003 {:GT "0/1", :HQ (3 3)}, :chr "19"})))
actual: (not (= nil ({:NA00001 {:GT "0|0", :HQ (10 10)}, :alt ["C"], :ref "A", :FORMAT (:GT :HQ), :NA00002 {:GT "0|0", :HQ (10 10)}, :pos 111, :filter nil, :id nil, :info nil, :qual 9.6, :NA00003 {:GT "0/1", :HQ (3 3)}, :chr "19"} {:NA00001 {:GT "0|0", :HQ (10 10)}, :alt ["G"], :ref "A", :FORMAT (:GT :HQ), :NA00002 {:GT "0|0", :HQ (10 10)}, :pos 112, :filter nil, :id nil, :info nil, :qual 10.0, :NA00003 {:GT "0/1", :HQ (3 3)}, :chr "19"})))
Testing cljam.io.wig-test
Testing cljam.test-common
Testing cljam.tools.cli-test
FAIL in (about-level) (cli_test.clj:171)
expected: (= (map (fn* [p1__35774#] (first (keep :LV (:options p1__35774#)))) (sam/read-alignments rdr)) test-sorted-bam-levels)
actual: (not (= () [{:type "i", :value 0} {:type "i", :value 1} {:type "i", :value 2} {:type "i", :value 2} {:type "i", :value 0} {:type "i", :value 0} {:type "i", :value 0} {:type "i", :value 1} {:type "i", :value 2} {:type "i", :value 3} {:type "i", :value 4} {:type "i", :value 5}]))
Testing cljam.util.chromosome-test
Testing cljam.util.intervals-test
Testing cljam.util.region-test
Testing cljam.util.sequence-test
Testing cljam.util.whole-genome-test
Testing cljam.util-test
Ran 328 tests containing 3587 assertions.
64 failures, 8 errors.
Ran tests.
Writing HTML report to: /Users/sohta/work/src/github.com/chrovis/cljam/target/coverage/index.html
|------------------------------+---------+---------|
| Namespace | % Forms | % Lines |
|------------------------------+---------+---------|
| cljam.algo.bam-indexer | 100.00 | 100.00 |
| cljam.algo.convert | 89.20 | 97.50 |
| cljam.algo.dedupe | 97.89 | 100.00 |
| cljam.algo.depth | 91.21 | 100.00 |
| cljam.algo.dict | 100.00 | 100.00 |
| cljam.algo.fasta-indexer | 100.00 | 100.00 |
| cljam.algo.level | 73.37 | 77.55 |
| cljam.algo.normal | 87.58 | 100.00 |
| cljam.algo.pileup | 96.97 | 99.52 |
| cljam.algo.sorter | 90.61 | 100.00 |
| cljam.algo.vcf-indexer | 100.00 | 100.00 |
| cljam.common | 100.00 | 100.00 |
| cljam.io.bam-index | 100.00 | 100.00 |
| cljam.io.bam-index.common | 100.00 | 100.00 |
| cljam.io.bam-index.core | 89.45 | 89.74 |
| cljam.io.bam-index.reader | 98.53 | 98.85 |
| cljam.io.bam-index.writer | 93.45 | 98.06 |
| cljam.io.bam.common | 100.00 | 100.00 |
| cljam.io.bam.core | 96.88 | 97.06 |
| cljam.io.bam.decoder | 94.16 | 98.37 |
| cljam.io.bam.encoder | 81.48 | 98.99 |
| cljam.io.bam.reader | 75.58 | 96.91 |
| cljam.io.bam.writer | 90.27 | 100.00 |
| cljam.io.bcf.reader | 91.21 | 94.40 |
| cljam.io.bcf.writer | 81.85 | 99.09 |
| cljam.io.bed | 90.36 | 93.02 |
| cljam.io.bigwig | 90.89 | 90.97 |
| cljam.io.cram.codecs.rans4x8 | 100.00 | 100.00 |
| cljam.io.cram.itf8 | 100.00 | 100.00 |
| cljam.io.csi | 72.48 | 98.91 |
| cljam.io.dict.core | 51.06 | 72.73 |
| cljam.io.dict.writer | 88.97 | 100.00 |
| cljam.io.fasta-index.core | 86.93 | 93.88 |
| cljam.io.fasta-index.reader | 95.00 | 100.00 |
| cljam.io.fasta-index.writer | 83.56 | 97.56 |
| cljam.io.fasta.core | 96.55 | 95.65 |
| cljam.io.fasta.reader | 86.06 | 94.90 |
| cljam.io.fasta.util | 98.36 | 100.00 |
| cljam.io.fasta.writer | 93.89 | 98.15 |
| cljam.io.fastq | 88.12 | 94.96 |
| cljam.io.gff | 91.96 | 100.00 |
| cljam.io.pileup | 89.13 | 100.00 |
| cljam.io.protocols | 100.00 | 100.00 |
| cljam.io.sam | 100.00 | 100.00 |
| cljam.io.sam.common | 100.00 | 100.00 |
| cljam.io.sam.reader | 71.47 | 82.19 |
| cljam.io.sam.util | 98.06 | 96.15 |
| cljam.io.sam.util.cigar | 94.71 | 98.94 |
| cljam.io.sam.util.flag | 100.00 | 100.00 |
| cljam.io.sam.util.header | 97.28 | 97.37 |
| cljam.io.sam.util.option | 89.93 | 91.46 |
| cljam.io.sam.util.quality | 87.44 | 87.50 |
| cljam.io.sam.util.refs | 100.00 | 100.00 |
| cljam.io.sam.util.sequence | 93.41 | 100.00 |
| cljam.io.sam.util.validator | 64.51 | 77.78 |
| cljam.io.sam.writer | 81.46 | 100.00 |
| cljam.io.sequence | 100.00 | 100.00 |
| cljam.io.tabix | 100.00 | 100.00 |
| cljam.io.twobit.reader | 78.29 | 94.41 |
| cljam.io.twobit.writer | 86.78 | 96.18 |
| cljam.io.util | 98.88 | 100.00 |
| cljam.io.util.bgzf | 84.98 | 95.24 |
| cljam.io.util.bgzf.gzi | 91.67 | 100.00 |
| cljam.io.util.bin | 99.61 | 100.00 |
| cljam.io.util.byte-buffer | 97.08 | 97.92 |
| cljam.io.util.chunk | 89.88 | 90.24 |
| cljam.io.util.lsb | 67.32 | 60.77 |
| cljam.io.util.lsb.data-io | 100.00 | 100.00 |
| cljam.io.util.lsb.io-stream | 98.74 | 98.88 |
| cljam.io.vcf | 95.69 | 95.89 |
| cljam.io.vcf.reader | 85.09 | 91.57 |
| cljam.io.vcf.util | 96.03 | 98.91 |
| cljam.io.vcf.util.check | 96.43 | 100.00 |
| cljam.io.vcf.util.normalize | 99.59 | 99.10 |
| cljam.io.vcf.util.validator | 87.94 | 95.75 |
| cljam.io.vcf.writer | 87.42 | 99.30 |
| cljam.io.wig | 91.15 | 92.14 |
| cljam.tools.cli | 64.19 | 76.50 |
| cljam.tools.main | 28.57 | 50.00 |
| cljam.util | 79.45 | 90.48 |
| cljam.util.chromosome | 95.97 | 100.00 |
| cljam.util.intervals | 95.35 | 97.67 |
| cljam.util.region | 100.00 | 100.00 |
| cljam.util.sequence | 57.85 | 100.00 |
| cljam.util.whole-genome | 100.00 | 100.00 |
|------------------------------+---------+---------|
| ALL FILES | 87.56 | 94.73 |
|------------------------------+---------+---------|
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment