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Pull requests: lh3/bwa

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Pull requests list

performance increase in alignment
#279 opened Apr 23, 2020 by andreasbuhr Loading…
7
set optimization from -O2 to -O3, 3.4 % performance increase observed
#278 opened Apr 22, 2020 by andreasbuhr Loading…
1
Update bwape.c to allow equal reads in pair to be mapped as mapped in proper pair
#259 opened Nov 25, 2019 by schultzdre Loading…
Fix potential assertion in bntseq fails #120
#243 opened Jun 25, 2019 by yanlinlin82 Loading…
1
fix incorrect secondary alignment in ksw_align
#227 opened Dec 5, 2018 by mirounga Loading…
bwa mem 20% speedup with vector instructions (Fixed intel-extend branch)
#226 opened Nov 24, 2018 by zamaudio Loading…
1
Add -C param for sampe/samse, to copy fastq comments into sam output
#203 opened May 30, 2018 by grahamgower Loading…
Proposed enhancement to the FAQ with a line for -M
#198 opened May 9, 2018 by mdkeehan Loading…
2
bwa mem: print qtip features
#156 opened Oct 17, 2017 by BenLangmead Loading…
1
bwa mem: read chunk size overflows for -t > 214
#155 opened Oct 17, 2017 by BenLangmead Loading…
Allow larger chunks of reads to be processed, and estimate the insert…
#106 opened Jan 29, 2017 by rbh Loading…
PPC64 patches
#71 opened Jun 10, 2016 by yhcheng Loading…
15
Bwa-Mem and tied pair-placements
#42 opened May 6, 2015 by boukn Loading…
mmap'ed access to reference files
#40 opened Jan 23, 2015 by ilveroluca Loading…
1
Add documentation describing the output format of out.hla.* files (doc fix only)
#39 opened Jan 5, 2015 by heuermh Loading…
3
Use allele instead of gene where appropriate (doc fix only)
#38 opened Jan 5, 2015 by heuermh Loading…
-q option to put seq/qual strings in secondary alignments
#36 opened Nov 12, 2014 by EReckase Loading…
Standard Fastq output for pemerge
#34 opened Oct 10, 2014 by a113n Loading…
Update bwape.c
#29 opened Jul 9, 2014 by earonesty Loading…
Fixed output, as newlines were missing.
#22 opened Feb 6, 2014 by jvhaarst Loading…
3
Added filenames to "Unmatched SAI magic" message
#20 opened Nov 12, 2013 by zestrada Loading…
Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2
#18 opened Jun 13, 2013 by mp15 Loading…
1
Adds check that ref sequence names do not contain semicolon during index
#16 opened May 20, 2013 by vsbuffalo Loading…
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…
3
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