6beab5f765
Merge branch 'master' into master_fixes
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Merge changes to commit c5434ac
2013-03-01 10:22:49 +00:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
4bb0bdddca
r306: introduce clipping penalty
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More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
e620f0ff4e
r302: updated the manpage
2013-02-27 13:16:22 -05:00
98787f0ae0
r295: generate NM
2013-02-26 13:36:01 -05:00
9957e04590
r278: don't perform too many mate-sw
2013-02-25 11:56:02 -05:00
5092211d75
controllable scoring matrix
2013-02-25 11:24:21 -05:00
5ead86acd3
optionally mark split hit as secondary
2013-02-25 11:18:35 -05:00
4dc982a3c7
support interleaved fastq
2013-02-25 00:13:32 -05:00
0b4a40dc25
updated revision number; to merge into master
2013-02-24 13:34:20 -05:00
85775c3384
output multiple hits
2013-02-24 13:23:43 -05:00
6bdccf2a8a
added a bit documentation
2013-02-24 13:09:29 -05:00
6e7903e9f3
added kopen support
2013-02-23 17:09:23 -05:00
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
67543f19a1
code refactoring
2013-02-23 15:55:55 -05:00
3c330d5049
for another round of code cleanup
2013-02-23 15:12:26 -05:00
d460f2ec9e
bugfix in multi-threaded bwa-mem
2013-02-23 14:48:54 -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
54da54ffd4
extend more seeds (and thus slower...)
2013-02-21 12:52:00 -05:00
66585b7982
code backup
2013-02-18 16:33:06 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
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I do not like many small files.
2013-02-12 10:36:15 -05:00
987d4b4205
fixed a stupid bug in fastq reading
2013-02-11 11:27:35 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
cb55617f50
added a new line
2013-02-08 22:12:18 -05:00
95a79afe71
command-line prompt
2013-02-08 22:11:44 -05:00
39607065e0
allow more seeds to be seen (thus slower..)
2013-02-08 16:56:28 -05:00
cd6bd524d4
discard internal seeds shorter than half
2013-02-07 19:50:37 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
d25a87cc50
code backup
2013-02-02 15:14:24 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
f8f3b7577a
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
620ad6e5b9
reseed long SMEMs
2013-02-01 14:20:38 -05:00
8977737460
basic chaining working
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Definitely suboptimal in a lot of corner cases...
2013-01-31 16:26:05 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
5a4a0c4173
a bit refactoring for further changes
2013-01-31 12:34:05 -05:00
6641788d38
preparation for further changes
2013-01-31 11:42:31 -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
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
Rob Davies
Heng Li