3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
cda85be059
fixed a couple bugs identified by gcc
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Recent gcc is better.
2013-02-23 17:15:07 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
cfa7165036
cleanup index loading code
2013-02-23 16:10:48 -05:00
904c3205c0
removed a few unused variables
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These variables have been assigned but never actually used. Reported by
gcc-4.7. Lower version cannot give such warnings.
2013-02-23 13:26:50 -05:00
f122fad562
minor code clean up
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bwtio.c is merged to bwt.c
2013-02-22 17:09:40 -05:00
6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
4f4e998d7f
Added wrappers for fputc and fputs; more efficient sequence printing
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Added wrappers err_fputc and err_fputs to catch failures in fput and fputs.
Macros err_putchar and err_puts call the new wrappers and can be used in
place of putchar and puts.
To avoid having to make millions of function calls when printing out
sequences, the code to print them in bwa_print_sam1 using putchar has
been replaced by a new version in bwa_print_seq that puts the sequence
into a buffer and then outputs the lot with err_fwrite. In testing, the
new code was slightly faster than the old version, with the added benefit
that it will stop promptly if IO problems are detected.
2013-01-09 14:43:36 +00:00
b081ac9b8b
Use wrapper functions to catch system errors
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Use the wrapper functions in utils.c plus a few extra bits of error
checking code to catch system errors and exit non-zero when they occur.
2012-12-16 10:34:57 +00:00
1cef219667
compute CIGAR; rev seq not working
2012-04-07 22:00:03 -04:00
66154ff5d2
towards refined gapped; unfinished
2012-04-07 01:25:39 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
a471f1918b
bugfix: long-existing out-of-boundary bug
2012-03-19 13:45:09 -04:00
dc4008936c
avoid duplicated XA tags
2011-11-19 14:52:47 -05:00
7664795ffb
fixed a minor issue about +/-1
2011-10-25 13:00:41 -04:00
aabb807734
concatenate for-rev sequences in the end
2011-10-25 11:22:08 -04:00
7b4266a6e5
bugfix: integer overflow and strand error in sampe
2011-10-24 17:07:12 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
243e735431
applied patches from Alec Wysoker
2011-05-04 09:46:50 -04:00
51d354cd28
Added barcode support
2011-01-15 15:35:39 -05:00
10721ca602
Added an option to accept Illumina 1.3+ fastq
2011-01-15 14:07:08 -05:00
f335b33624
fixed a bug in bwase: no RG for unmapped read pairs
2011-01-15 10:32:45 -05:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Rob Davies
Heng Li
Heng Li