cancerit/PCAP-core

Issues

• a installation error

  #70 opened 2 years ago by wul99
  0

• bam_stats fails to give informative error on BAMs with no RG lines/tags

  #66 opened 3 years ago by leovam
  8

• bam_stats - passthrough (CRAM)

  #12 opened 4 years ago by keiranmraine
  2

• Ensure builds on alpine

  #10 opened 4 years ago by keiranmraine
  1

• Is it worth breaking up bwa_mem.pl into more steps?

  #61 opened 4 years ago by jsmedmar
  3

• bwa_mem.pl - bwamem step needs to delete bamsort tmp files if retry

  #60 opened 4 years ago by keiranmraine
  1

• does the output depend on the input file format?

  #52 opened 4 years ago by mgcam
  3

• mapped merge

  #46 opened 4 years ago by keiranmraine
  3

• Support for Illumina's FASTQ file format

  #44 opened 5 years ago by ckandoth
  3

• MismatchQC - C version

  #7 opened 7 years ago by keiranmraine
  1

• support for irods: protocol

  #53 opened 5 years ago by mgcam
  0

• C: Makefile should work with htslib installation

  #48 opened 5 years ago by keiranmraine
  0

• should not use '\t' as header separator

  #47 opened 5 years ago by byb121
  0

• bwa_mem.pl -p stats not doing anything on new versions

  #45 opened 5 years ago by jsmedmar
  8

• bamsort sortthreads

  #42 opened 6 years ago by mflevine
  1

• map_threads should use all cores if possible

  #41 opened 6 years ago by jsmedmar
  1

• fragment variable usage is inconsistant

  #39 opened 6 years ago by keiranmraine
  1

• Speed up job resume (Threaded.pm)

  #40 opened 6 years ago by keiranmraine
  2

• Move sync after chmod

  #31 opened 6 years ago by keiranmraine
  3

• Threaded.pm - thread_join_interval

  #30 opened 6 years ago by keiranmraine
  1

• Improve yaml to make paired read processing more robust

  #29 opened 6 years ago by keiranmraine
  1

• “multiple target patterns. Stop.” when installing PCAP

  #24 opened 6 years ago by Liulab
  1

• cover: command not found

  #26 opened 6 years ago by WortJohn
  1

• add psmisc to install dependencies

  #23 opened 6 years ago by jsmedmar
  5

• fragment parameter has no default although it's listed as optional

  #25 opened 6 years ago by jsmedmar
  0

• Failed setup.sh

  #21 opened 7 years ago by looxon93
  11

• CI: Add small exec of fq, bam and cram

  #22 opened 7 years ago by keiranmraine
  4

• diff_bams add threadPool

  #19 opened 7 years ago
  0

• bam_stats - add thread pool

  #18 opened 7 years ago by keiranmraine
  0

• diff_bams - should give non-zero exit when different

  #16 opened 7 years ago by keiranmraine
  0

• Pre-release from feature branch

  #9 opened 7 years ago by keiranmraine
  1

• phase out use of biobambam2

  #14 opened 7 years ago by keiranmraine
  0

• Metadata for RG headers

  #6 opened 7 years ago by keiranmraine
  1

• bam_stats - qcfail reads

  #8 opened 7 years ago by keiranmraine
  3

• Test of perl threading incorrect

  #5 opened 7 years ago by keiranmraine
  0

• bam_stats: no mapped reads results in header only bas file

  #4 opened 7 years ago by keiranmraine
  1

• threaded backoff: bad pattern match

  #3 opened 8 years ago by keiranmraine
  0