6ba11ab68c
no effective changes
2013-02-07 16:42:01 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
27fdf6397d
single-end working! no mapQ, though
2013-02-07 15:52:36 -05:00
49f2bcc015
CIGAR is wrong, but the rest is okay
2013-02-07 14:57:22 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -05:00
bfeb37c4de
code backup
2013-02-07 13:29:01 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
a09db69037
In bwtsw, replace the batch seq-reader with bseq
2013-02-06 17:12:27 -05:00
901d28d5f5
code backup
2013-02-06 15:03:09 -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
e65b2096f7
removed useless members
2013-02-06 12:25:49 -05:00
797a8c147e
sorting chains while filtering chains
2013-02-05 21:58:33 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
14e6a7bdb9
fixed a silly bug in ksw_extend()
...
Query return value is assigned to the target variable and vice versa...
2013-02-05 17:29:03 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
86caae811e
added comments
2013-02-05 16:58:35 -05:00
1bc9712cd8
explicitly use bit to keep bt matrix
...
This also simplifies backtracking.
2013-02-05 16:28:15 -05:00
7e1466c885
implemented NW backtrack
2013-02-05 16:05:53 -05:00
d91e320972
towards reimplementing banded NW alignment
2013-02-05 12:06:56 -05:00
7067af833d
fixed a silly bug on sorted merge
2013-02-05 00:41:07 -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
c589b42fb5
minor tuning for fewer identical hits
2013-02-04 16:48:11 -05:00
29c8546679
better ref extraction
2013-02-04 16:08:00 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
f27bd18f20
check if every seed is included; not used for now
2013-02-04 15:09:47 -05:00
5bfa45a69b
write the mem_aln_t struct
2013-02-04 15:02:56 -05:00
666638a953
changed the default scoring
2013-02-04 14:51:51 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
f83dea36d8
no effective changes
2013-02-03 18:16:43 -05:00
2093398231
bugfix: the first line is wrong
2013-02-03 17:47:57 -05:00
e8a1962efe
code backup; it is wrong
2013-02-03 17:25:40 -05:00
92b084e553
reimplemented SW extension; not tested yet
2013-02-02 16:38:21 -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
7ab4b3321f
bugfix: memory leak
2013-02-01 15:26:34 -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
abc675f278
typo in comments
2013-02-01 13:14:16 -05:00
86f2e134ba
no effective changes
2013-02-01 12:57:48 -05:00
5d372cef65
bugfix: wrong B-tree comparison
2013-01-31 16:39:24 -05:00
8977737460
basic chaining working
...
Definitely suboptimal in a lot of corner cases...
2013-01-31 16:26:05 -05:00
6c19c9640c
code backup
2013-01-31 15:55:22 -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
6de74888fd
bugfix: min_intv not working in SMEM
2013-01-31 12:12:58 -05:00
543c719a54
fixed a couple of unimportant bugs in SMEM
2013-01-31 11:53:07 -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
...
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
Heng Li
Rob Davies