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Pull requests list

Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2
#18 opened Jun 13, 2013 by mp15 Loading… updated Jun 12, 2014
1
Initial public release cilk version of aln.
#23 opened Feb 10, 2014 by caherzee Loading… updated Jun 12, 2014
Added filenames to "Unmatched SAI magic" message
#20 opened Nov 12, 2013 by zestrada Loading… updated Jun 13, 2014
Fixed output, as newlines were missing.
#22 opened Feb 6, 2014 by jvhaarst Loading… updated Jun 13, 2014
3
Adds check that ref sequence names do not contain semicolon during index
#16 opened May 20, 2013 by vsbuffalo Loading… updated Jul 5, 2014
Update bwape.c
#29 opened Jul 9, 2014 by earonesty Loading… updated Jul 9, 2014
Adding a flag to sampe (-d) to disable pair rescuing if too many rescue attempts are made.
#12 opened Sep 30, 2012 by drio Loading… updated Jul 9, 2014
3
Standard Fastq output for pemerge
#34 opened Oct 10, 2014 by a113n Loading… updated Oct 10, 2014
-q option to put seq/qual strings in secondary alignments
#36 opened Nov 12, 2014 by EReckase Loading… updated Nov 12, 2014
Use allele instead of gene where appropriate (doc fix only)
#38 opened Jan 5, 2015 by heuermh Loading… updated Jan 5, 2015
Bwa-Mem and tied pair-placements
#42 opened May 6, 2015 by boukn Loading… updated May 6, 2015
mmap'ed access to reference files
#40 opened Jan 23, 2015 by ilveroluca Loading… updated Jun 8, 2016
1
Allow larger chunks of reads to be processed, and estimate the insert…
#106 opened Jan 29, 2017 by rbh Loading… updated Aug 28, 2017
bwa mem: read chunk size overflows for -t > 214
#155 opened Oct 17, 2017 by BenLangmead Loading… updated Oct 17, 2017
bwa mem: print qtip features
#156 opened Oct 17, 2017 by BenLangmead Loading… updated Nov 1, 2017
1
Add -C param for sampe/samse, to copy fastq comments into sam output
#203 opened May 30, 2018 by grahamgower Loading… updated May 30, 2018
Fix typo: Malformated → Malformed
#212 opened Aug 2, 2018 by tskir Loading… updated Aug 2, 2018
fix incorrect secondary alignment in ksw_align
#227 opened Dec 5, 2018 by mirounga Loading… updated Dec 5, 2018
Proposed enhancement to the FAQ with a line for -M
#198 opened May 9, 2018 by mdkeehan Loading… updated Apr 2, 2019
2
bwa mem 20% speedup with vector instructions (Fixed intel-extend branch)
#226 opened Nov 24, 2018 by zamaudio Loading… updated Jun 5, 2019
1
Fix potential assertion in bntseq fails #120
#243 opened Jun 25, 2019 by yanlinlin82 Loading… updated Jun 28, 2019
1
Windows Subsystem for Linux (WSL) FAQ
#264 opened Dec 29, 2019 by karolzlot Loading… updated Dec 29, 2019
Add documentation describing the output format of out.hla.* files (doc fix only)
#39 opened Jan 5, 2015 by heuermh Loading… updated Apr 22, 2020
3
PPC64 patches
#71 opened Jun 10, 2016 by yhcheng Loading… updated May 17, 2020
15
set optimization from -O2 to -O3, 3.4 % performance increase observed
#278 opened Apr 22, 2020 by andreasbuhr Loading… updated May 22, 2020
1
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