752ce69b78
Added more wrappers for functions that make system calls
...
Added the following wrappers that check the results of system calls
and exit non-zero if something went wrong. This is so bwa can be more
robust against system failures (e.g. IO errors from remote storage, or
running out of memory). The existing and new wrappers have also been
modified so that they no longer try to dump core on failure. In most cases
the resulting core files are not useful (especially if bwa was compiled
with optimization turned on) so just pollute whatever directories they
got written to.
Wrappers for memory allocation functions:
xcalloc
xmalloc
xrealloc
xstrdup
New wrappers for IO functions:
err_fread_noeof (also dies on EOF)
err_gzread
err_fseek
err_rewind
err_ftell
2012-12-16 10:05:32 +00:00
292f9061ab
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
3abfd0743a
r131: r128 plus remote changes
2012-06-28 14:52:18 -04:00
fa51f029b9
Merge branch 'master' of github.com:lh3/bwa
2012-06-28 14:51:51 -04:00
f44edd4fc9
r128: more conservative chaining filter
2012-06-28 14:51:02 -04:00
0ae318be0d
resolve duphits after right extension as well
2012-06-28 13:32:58 -04:00
f89649ee26
Merge pull request #11 from sjackman/inline
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Do not inline functions used externally
2012-06-26 07:02:49 -07:00
84d34e1d0b
Do not inline functions used externally
...
Compiling using CLANG gives the following errors:
Undefined symbols for architecture x86_64:
"_bwt_occ", referenced from:
_bwt_cal_sa in bwt.o
_bwt_sa in bwt.o
"_bwt_2occ", referenced from:
_bwt_match_exact in bwt.o
_bwt_match_exact_alt in bwt.o
_bwt_cal_width in bwtaln.o
"_bwt_2occ4", referenced from:
_bwt_match_gap in bwtgap.o
_bsw2_core in bwtsw2_core.o
"_bwtl_2occ4", referenced from:
_bsw2_core in bwtsw2_core.o
2012-06-25 12:48:43 -07:00
09ee115dcc
r126: release bwa-0.6.2
2012-06-19 13:29:44 -04:00
29ed2d8287
rename the "api" branch as "master"
2012-06-19 13:13:29 -04:00
d97ff6bf72
r124: updated version number
2012-04-17 20:45:07 -04:00
72f1a95448
Merge branch 'master' into api
2012-04-17 20:44:30 -04:00
cd818687ac
r115: added -I and -S to bwasw
2012-04-17 20:43:43 -04:00
4f61e2b7f5
unnecessary large .sai output
2012-04-17 19:31:37 -04:00
9c486fa41e
updated APIs abit
2012-04-08 00:55:52 -04:00
3b5a9e5595
simplified bwa_se() interface
2012-04-08 00:12:34 -04:00
ca93a71e6e
complete single-end alignment
2012-04-08 00:02:06 -04:00
080726cb47
preliminary doc
2012-04-07 22:50:07 -04:00
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
a1abfe9977
API: aln seems working
2012-04-07 00:23:01 -04:00
cff473393c
commented out debugging code
2012-04-02 12:05:15 -04:00
790df95e1a
updated revision number
2012-04-02 11:43:32 -04:00
36f2fd6238
bugfix: incorrect bandwidth
2012-04-02 11:39:40 -04:00
d3169804f6
debugging; bug persistant
2012-04-02 10:45:42 -04:00
173b93dfd4
debugging code: bwasw has a rare bug
2012-04-02 09:37:02 -04:00
d33abf127f
check *.64.bwt first and then *.bwt
2012-03-29 14:45:00 -04:00
c875085b2b
do not use .64 suffix by default
2012-03-29 12:31:01 -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
91a4a0c8ea
Release bwa-0.6.1
2011-11-28 09:52:07 -05:00
64e353ce49
bugfix: bwa-sw PE segfault in rare case
2011-11-28 09:12:21 -05:00
bf65b6463a
fastmap: optionally output the original query seq
2011-11-24 19:44:21 -05:00
150bfbdef4
fixed a deadlock; SMEM iterator
2011-11-24 19:15:14 -05:00
b5170e0efa
output the NM tag
2011-11-24 11:51:38 -05:00
717959e819
fixed a minor issue in trimming
2011-11-24 10:39:41 -05:00
eeedda105d
perhaps improves samse/sampe
2011-11-24 01:22:02 -05:00
196b50dde3
optionally mark multi-part hits as secondary
2011-11-23 23:39:59 -05:00
9f84384ed2
reordering BWA-SW command-line prompt
2011-11-23 23:36:08 -05:00
b17b6577ac
removed a useless bwa-sw CMD option
2011-11-23 23:30:14 -05:00
107a9870ef
incorrect mate pos in BWA-SW SE mode
2011-11-23 23:18:51 -05:00
dec584d50b
fixed a long-existing bug in trimming
2011-11-23 23:11:50 -05:00
84aa3fa696
useless script
2011-11-19 21:48:54 -05:00
182cb2e89c
use standard SW when no SSE2
2011-11-19 19:38:21 -05:00
dc4008936c
avoid duplicated XA tags
2011-11-19 14:52:47 -05:00
8f89f55484
fixed a segfault when there are too few good bases.
2011-11-17 22:13:38 -05:00
c8edcafb44
added SEAL
2011-11-12 20:48:35 -05:00
162f220deb
updated README
2011-11-12 20:26:52 -05:00
9f2c77880d
remove a useless file
2011-11-12 20:06:37 -05:00
770a5f2ae0
Release BWA-0.6.0
2011-11-12 20:04:39 -05:00
Rob Davies
Heng Li
Heng Li
Shaun Jackman