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mariokostelac / run_args.txt
Created August 28, 2015 16:38
# version: 6a90598-dirty
#/Users/mario/assembly-tools/bin/layout --overlaps_format=mhap -r /Users/mario/assembly-tools/npore_ecolli_reads/reads-nmeth-all_2d.fasta -x overlaps.mhap -v 1
# filter reads parameters
READS_MIN_LEN: 3000
# trimming parameters
READ_LEN_THRESHOLD: 100000
MAX_READS_IN_TIP: 2
MAX_DEPTH_WITHOUT_EXTRA_FORK: 5
@mariokostelac
mariokostelac / remove_closing_tags.sh
Last active August 29, 2015 14:05 — forked from lorenzo/remove_closing_tags.sh
#!/bin/bash
# vim:ft=sh:ts=3:sts=3:sw=3:et:
###
# Strips the closing php tag `?>` and any following blank lines from the
# end of any PHP file in the current working directory and sub-directories. Files
# with non-whitespace characters following the closing tag will not be affected.
#
# Author: Bryan C. Geraghty <bryan@ravensight.org>
# Date: 2009-10-28
@mariokostelac
mariokostelac / panic
Created August 25, 2014 09:16
panic: nil
goroutine 18 [running]:
runtime.panic(0x0, 0x0)
/usr/lib/go/src/pkg/runtime/panic.c:266 +0xb6
github.com/backplane/platform/servercomm.func<C2><B7>005()
/home/vagrant/go/src/github.com/backplane/platform/servercomm/subscription_test.go:57 +0x29
created by time.goFunc
/usr/lib/go/src/pkg/time/sleep.go:123 +0x47
@mariokostelac
mariokostelac / subscription.go
Created August 25, 2014 09:17
package servercomm
import (
"sync"
"time"
)
type Subscription struct {
sync.Mutex
id int64
@mariokostelac
mariokostelac / subscription.go
Last active August 29, 2015 14:05
package servercomm
import (
"sync"
"time"
)
type Subscription struct {
sync.Mutex
id int64
@mariokostelac
mariokostelac / influenza-A.seq
Created November 13, 2014 21:30
>gnl|ti|1086975905 name:1099575910428 mate_pair:1086975851
TGGAAATCCGTCTCGAATGGAGGTCTAGTGCGTTTCCGCTTCAACCCGATGATTGTCGAACTTGCAGAAA
AAGCAATGAAAGAGTATGGAGAGGATCTGAAAATTGAAACAAACAAATTTGCAGCAATATGCACCCACTT
GGAGGTATGTTTCATGTATTCAGATTTTCATTTCATCAATGAACAAGGCGAATCAATAATGGTAGAACTT
GATGATCCAAATGCACTGTTAAAGCACAGATTTGAAATAATCGAGGGGAGAGACAGAACAATGGCCTGGA
CAGTAGTAAACAGTATCTGCAACACTACTGGAGCTGAAAAACCGAAGTTTCTACCAGATTTGTATGATTA
CAAGGAGAACAGATTCATCGAAATTGGAGTGACAAGAAGAGAAGTCCACATATATTACCTTGAAAAGGCC
AATAAAATTAAATCTGAGAACACACACATTCACATTTTCTCATTCACTGGGGAGGAAATGGCCACAAAGG
CAGACTACACTCTCGACGAGGAGGTCATAGCTGTTTACTGAGGGACCCATTTAAAATTCTAATACCCAGC
TTTGAACGTGACCATGCCAAACAAGGACAACCTGACCACACAAGAGGTCAA
@mariokostelac
mariokostelac / contigs.minimus
Created January 8, 2015 19:27
minimusov rezultat nad influenza-A
>1
CAATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCA
CTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACAT
CGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATACC
CAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAATGAACAAGGACAAA
CTCTATGGAGTAAAATGAGTGATGCTGGATCAGATCGAGTGATGGTATCACCTTTGGCTG
TAACATGGTGGAATAGAAATGGACCCGTGACAAGTACGGTCCATTACCCAAAAGTATACA
AGACTTATTTTGACAAAGTCGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTA
GAAATCAAGTCAAGATACGCAGAAGAGTAGACATAAACCCTGGTCATGCAGACCTCAGTG
CCAAAGAGGCACAAGATGTAATTATGGAAGTTGTTTTTCCCAATGAAGTGGGAGCCAGGA
@mariokostelac
mariokostelac / contigs.we
Created January 8, 2015 19:28
nas rezultat nad influenza-A
>1
CAATTATATTnAGTATGGAAGATAAAAGAACTACGnnGAATCTGATGTCGCAGTCnnTCn
nGCACTCGCGAGATACTGACnnAnAAAAnCCACAGTGGACCATATGGCCATAATTAAGnA
AGTACnACATCGnnGGGnAGACAGGAAAAGAACCCGTCACTTAGGATGAAnATGGAnTGn
ATGGCAATGAnAATnACCCAATCACTGnCTGACnnAnAAAnGGATAACAGAAATGGTTCC
GGAGAGAAATGAACnAAGGACAAnACTCTATGGAGTAAAATGAGnTGAnTGCTGGATCAG
ATCGAGnTnGAnTGGTATCAnCnCTTTGGCTGTAACATGGTGGAATAGAAATGGACCCGT
GACAAGTnACGnGTCCATTACCCAAAAGTATACAnnAGACTTnAnTTnTTnnGACAAAGT
CGAAAGGTTAAAACATGGAACCTTTGGCCCTGTTCATTTTAGAAATCAAGTCAAGATnAC
GCnAnGAAGAGTAGnAnnCATAAACCCTGGTCATGCAnGnAnnCCTCAGTGCCAAAGAGG
@mariokostelac
mariokostelac / contigs.minimus
Created January 8, 2015 19:28
minimusov rezultat nad zgene
>1
AGAGTGCAGAGCAACAAAAACAGCATACAGAAGTATAAATGCACAGTTACGCGCAAGACA
GGTGCTGTGGGTCACGGCAATCACTCGACACAGAAGTATAAACCAGCCCTAACCCCGGCA
TCCTGGCCAAATTACCTCCGGTCCTTACCCATCATGGCCTCCCAATCATCCCCATCCACC
AAATTAGCTGTATCACTTTCTCTTCACTCCACCTATAGCTGGTGTGTGGTGAGCGCACTG
GCGCTGTTGTCATGTTGGTACGGTCACATCATCCAAGTGGATTCTGCACACTGGGGGTGG
TGTGAAGGGATCCCTGTCATGATTGTGGAGCTCTTTGGGTGTATGGCCATACACGATAAA
TGGGCTACATAAATACACACATATTACATTTCAGCACATTATCACTGTGGTGTTGAAATG
TAACTAAAATCAAACTTTATAGTTACTCAATCTCTCTTTTCTGTCTTTTTTCAGAGGCTT
TTGACATGGTGCTTCGTCTGGGCCGTAATTCCACTCTGATGGTGTTACGCGAGGAGTTTC
@mariokostelac
mariokostelac / contigs.we
Created January 8, 2015 19:28
nas rezultat nad zgene
>1
TTTTTCTTATTTTTCCTTTGTTTTTTTTGATTGTTTGGGTTTTTACCAAAATCTGGTTTC
ATTTCAAGCAGCTCCATTTTGAATATTTTCCCCAGAAAAACAAAAATAAAAAACAAGATA
TGTTGAATGCTTATTTCCCCCACTGTAAGTAAGTTCTTTATGCAAACTTGACACATTTTT
TCGACCAAATCAAAAGTAATGTTGTACAATGCATTCAATTGGTTGGACTCGTGTTATATT
ACCATCAATCATATTTTCATCAGnCACCAnACTGAAAAATTCTTCCAACAGACAAAAATC
CTTGGGAAAACATGAGCTTTGAAAATTAAATGTGACCTTAAGCTATTCCAAATTATTTAT
CAGGCTATACTCATTCCCTTGTGCGCTCATTTTTATTTACACATGCCATGTACCTTGGCA
AGGCTCCAAAGTAACCACAATGATGTGGAACAGTTATTCTGCACCGCTGCAAGCATACAG
AAGAACTATTAATCTTAGTTTACATGTCTGCAAACTGAATGACGCCACCTAATGAACTTA