8a078cc16d
Merge branch 'master' into master_fixes
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
d35f33b513
r316: don't allocate zero-length memory
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It is not a bug, but Electric Fence does not like that.
2013-03-04 10:22:18 -05:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
61dd3bf13a
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
5f8c6efbc3
forbid x-bounary bns_get_seq(); code backup
2013-02-16 09:48:44 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
55f1b36534
New wrapper for gzclose; added err_fflush calls and made it call fsync too.
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Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.
Put in some more err_fflush calls before files being written are closed.
Made err_fflush call fsync. This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned. If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
2013-01-03 16:57:37 +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
8f89f55484
fixed a segfault when there are too few good bases.
2011-11-17 22:13:38 -05:00
aabb807734
concatenate for-rev sequences in the end
2011-10-25 11:22:08 -04:00
ca809a44d9
build .pac in memory; prepare for further changes
2011-10-25 10:27:13 -04:00
7626595e3a
backup the current debugging code; more changes
2011-10-25 10:03:57 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
fe9da3c704
allow to pac forward strand only
2011-10-21 10:57:12 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
2d2db5d50f
aln seems working
2011-10-20 16:13:35 -04:00
46123639cf
removed reverse pac; bwa is not working right now
2011-10-20 12:09:35 -04:00
70da24e177
restructure bns_fasta2bntseq() for further changes
2011-10-20 11:53:44 -04:00
72563c38f3
automatically choose the algorithm for BWT
2011-06-09 17:33:25 -04:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Rob Davies
Heng Li
Heng Li