I hereby claim:
- I am chapmanb on github.
- I am chapmanb (https://keybase.io/chapmanb) on keybase.
- I have a public key whose fingerprint is B033 B3DB 73C2 76A1 CC1F 5560 8B28 0C00 2059 4258
To claim this, I am signing this object:
Brad Chapman chapmanb
chapmanb
/ adam-clojure-deps.txt
Last active
August 29, 2015 13:57
Debugging Clojure calling ADAM: dependencies and traceback error
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| [clojure-complete "0.2.3" :exclusions [[org.clojure/clojure]]] | |
| [edu.berkeley.cs.amplab.adam/adam-cli "0.7.1"] | |
| [args4j "2.0.23"] | |
| [org.scala-lang/scala-library "2.10.3"] | |
| [org.slf4j/slf4j-log4j12 "1.7.5"] | |
| [log4j "1.2.17"] | |
| [org.slf4j/slf4j-api "1.7.5"] | |
| [edu.berkeley.cs.amplab.adam/adam-core "0.7.1"] | |
| [cofoja "1.0"] | |
| [com.twitter/parquet-avro "1.3.2"] |
chapmanb
/ hsph05_status.txt
Created
April 7, 2014 09:56
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| 60252 bchapman 20 0 14732 2108 944 R 100.0 0.0 27:12.14 bcftools | |
| 61094 bchapman 20 0 14592 2056 940 R 100.0 0.0 11:02.15 bcftools | |
| 61151 bchapman 20 0 14708 2088 944 R 100.0 0.0 10:11.72 bcftools | |
| 61156 bchapman 20 0 14552 1944 944 R 100.0 0.0 9:54.70 bcftools | |
| 61203 bchapman 20 0 14552 1964 944 R 100.0 0.0 9:36.42 bcftools | |
| 61207 bchapman 20 0 14552 1952 944 R 100.0 0.0 9:30.39 bcftools | |
| 61212 bchapman 20 0 20832 8184 944 R 100.0 0.0 9:28.28 bcftools | |
| 61224 bchapman 20 0 14556 1952 944 R 100.0 0.0 9:22.26 bcftools | |
| 61225 bchapman 20 0 14556 1972 944 R 100.0 0.0 9:23.08 bcftools | |
| 61227 bchapman 20 0 20844 8220 944 R 100.0 0.0 9:22.24 bcftools |
chapmanb
/ sv_ensemble_counts.txt
Last active
August 29, 2015 14:02
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| $ wc -l ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | |
| 79 ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | |
| $ grep DEL NA12878-ensemble-lumpy.bed | bedtools intersect -a stdin -b ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | wc -l | |
| 39 | |
| $ grep DEL NA12878-ensemble-lumpy.bed | bedtools intersect -v -a stdin -b ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | wc -l | |
| 57 | |
| $ grep DEL NA12878-ensemble-delly.bed | bedtools intersect -a stdin -b ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | wc -l | |
| 31 | |
| $ grep DEL NA12878-ensemble-delly.bed | bedtools intersect -v -a stdin -b ../NA12878.50X.ldgp.molpb_val.20140508.chr21.bed | wc -l | |
| 21 |
chapmanb
/ FindSomatic.pl
Last active
August 29, 2015 14:02
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| #!/usr/bin/perl | |
| ################################################################### | |
| # FindSomatic.pl | |
| # | |
| # Tool for detecting somatic mutations in normal/tumor pair | |
| # using microassembly | |
| # | |
| # Author: Giuseppe Narzisi | |
| # Date: December 11, 2013 |
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| 1 | |
| 2 0 10592 | |
| 2 13946 13963 | |
| 2 31973 32405 | |
| 2 37429 38219 | |
| 2 52511 52548 | |
| 2 62286 62336 | |
| 2 64511 64532 | |
| 2 69462 69482 | |
| 2 87327 88553 |
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| diff --git a/HashesIO.pm b/HashesIO.pm | |
| index 7738511..8c37d83 100644 | |
| --- a/HashesIO.pm | |
| +++ b/HashesIO.pm | |
| @@ -342,7 +342,7 @@ sub loadDB { | |
| #if ($chr =~ /chr\w*(\w+)/) { $variants{$key}->{chr} = $1; } | |
| if($intarget) { # export if intarget true | |
| - next if(sget($mut, $exons) eq "false"); | |
| + next if(inTarget($mut, $exons) eq "false"); |
chapmanb
/ tophat_samtools_10.diff
Created
September 8, 2014 09:39
Support for samtools 1.0 in tophat
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| --- a/tophat 2014-06-24 10:15:55.000000000 -0400 | |
| +++ b/tophat 2014-09-08 05:33:49.818129478 -0400 | |
| @@ -1537,8 +1537,12 @@ | |
| samtools_out = proc.communicate()[1] | |
| # Find the version identifier | |
| - version_match = re.search(r'Version:\s+(\d+)\.(\d+).(\d+)([a-zA-Z]?)', samtools_out) | |
| - samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]] | |
| + version_match = re.search(r'Version:\s+(\d+)\.(\d+).(\d+)?([a-zA-Z]?)', samtools_out) | |
| + samtools_version_arr = [int(version_match.group(x)) for x in [1,2]] |
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| ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDEtX2XnM6o3ibDFpk08sNOXAAV7z86CBKDM5mdf8czHZrb8Gybvq3ZOb05UbZVbMHZpwIOMPRdni7LZON0u4ZwiXCRN7ma48gTm37AGOvq0UQu2ygXU6QL64CrZrSRyjf3EU+ch6An20YY0/mGnCfzA3dE3uRU+1JjCy3A+3sakrVmUe3HJmPNXdD09sfXOWlK0GgEtgdOLUfWKqq4EZ4xdDpeTSDCvY1J5+3ATqA17Wen15D9A8eH6JsEw5JOB6BvqMQ/2rF3dCNaOBweXKZo5MlpS021lexFWhL8ebHm7Zmr+pGsjrJpijG/88AcqRyohqnJQoW6QcUTgsbyozSv chapmanb@kunkel |
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| ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDuoJah9EsGNkSeLDtGezs1N0Cp4n0sXcEh5C0JIcyo+ozWlIjYayMft+AUPS9rccyazwjPrP5qVNpD1J767/9/Z9z1yQZVNtC/7SDis86M/SkOaaRS8g/K31A7g5/O4ErJRyxjoxraRH1/E7Tsyyyh1SjsHucmkkx9xQL1iH8I8zu+9DNtIeIinYzvDkeCR8Piz1FXzEdbfHgrjGK9XrlljVcdquq7ky705uNIci6kHIPcBSlmS5QZDMqj+r+6tk42ixu4EQTz74lqWmzdZzoHkbBP00aYOliidcpsMAZ6/mekuFtlDUB5xddlH/LHFIta9FZRA2TyiTaJae/r+SP1 chapmanb@kunkel |
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