All pull requests

Pull requests

• Badges for usegalaxy.org and usegalaxy.eu

  #448·nekrut opened Oct 14, 2025·

  ·

• performance increase in alignment

  #279·andreasbuhr opened Apr 23, 2020·

  ·
  7

• set optimization from -O2 to -O3, 3.4 % performance increase observed

  #278·andreasbuhr opened Apr 22, 2020·

  ·
  1

• Update bwape.c to allow equal reads in pair to be mapped as mapped in proper pair

  #259·schultzdre opened Nov 25, 2019·

  ·

• Fix potential assertion in bntseq fails #120

  #243·yanlinlin82 opened Jun 25, 2019·

  ·
  1

• fix incorrect secondary alignment in ksw_align

  #227·mirounga opened Dec 5, 2018·

  ·

• bwa mem 20% speedup with vector instructions (Fixed intel-extend branch)

  #226·zamaudio opened Nov 24, 2018·

  ·
  1

• Add -C param for sampe/samse, to copy fastq comments into sam output

  #203·grahamgower opened May 30, 2018·

  ·

• Proposed enhancement to the FAQ with a line for -M

  #198·mdkeehan opened May 9, 2018·

  ·
  2

• bwa mem: print qtip features

  #156·BenLangmead opened Oct 17, 2017·

  ·
  1

• bwa mem: read chunk size overflows for -t > 214

  #155·BenLangmead opened Oct 17, 2017·

  ·

• Allow larger chunks of reads to be processed, and estimate the insert…

  #106·rbh opened Jan 29, 2017·

  ·

• PPC64 patches

  #71·yhcheng opened Jun 10, 2016·

  ·
  15

• Bwa-Mem and tied pair-placements

  #42·boukn opened May 6, 2015·

  ·

• mmap'ed access to reference files

  #40·ilveroluca opened Jan 23, 2015·

  ·
  1

• Add documentation describing the output format of out.hla.* files (doc fix only)

  #39·heuermh opened Jan 5, 2015·

  ·
  3

• Use allele instead of gene where appropriate (doc fix only)

  #38·heuermh opened Jan 5, 2015·

  ·

• -q option to put seq/qual strings in secondary alignments

  #36·EReckase opened Nov 12, 2014·

  ·

• Standard Fastq output for pemerge

  #34·a113n opened Oct 10, 2014·

  ·

• Update bwape.c

  #29·earonesty opened Jul 9, 2014·

  ·

• Fixed output, as newlines were missing.

  #22·jvhaarst opened Feb 6, 2014·

  ·
  3

• Added filenames to "Unmatched SAI magic" message

  #20·zestrada opened Nov 12, 2013·

  ·

• Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2

  #18·mp15 opened Jun 13, 2013Contributor·

  ·
  1

• Adds check that ref sequence names do not contain semicolon during index

  #16·vsbuffalo opened May 20, 2013·

  ·

• Adding a flag to sampe (-d) to disable pair rescuing if too many rescue attempts are made.

  #12·drio opened Sep 30, 2012·

  ·
  3