c56c2e4677
Several trivial Debian patches
...
[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling
[Fabian Klötzl]
change printing as size_t is unsigned
2017-07-04 21:24:15 +01:00
bc58bf265d
Add "bwa mem -o FILE" synonym and documentation
...
As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.
2017-06-27 17:05:44 +01:00
d28da05f36
Added option to write output to file
2017-06-27 16:47:13 +01:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
1e6a10ce2d
a typo in fastmap command-line prompt
2016-02-01 11:41:46 -05:00
1247dc2346
removed the pbread mode
...
It is not working well. Not at all.
2016-01-26 22:37:01 -05:00
ed95769a33
updated documentations
...
(prepare for release)
2014-12-21 16:30:29 -05:00
925ddfb697
r1025: accept file with -H; allow to replace @SQ
2014-12-11 10:38:36 -05:00
9d8c906e4c
r1017: process I/O in a separate thread
...
Previously, bwa-mem waits for I/O. When the input data comes from a slow source
(I/O or piped from a slow program), bwa-mem may spend significant amount of
wall-clock time in the single-thread mode. The same may also happen when bwa-mem
writes to slow target. This commit uses two sequence buffers. it allows bwa-mem
to map one buffer while filling or dumping the other buffer. When bwa-mem is run
on 16 threads using the bwa.kit pipeline, the wall clock time is reduced by 30%.
2014-11-26 12:32:48 -05:00
b5f6ed3020
r1005: insert arbitrary header lines
2014-11-19 10:59:05 -05:00
80e4ecfa79
r998: smart pairing; allow mixture of SE/PE reads
2014-11-18 14:30:22 -05:00
9bf898fa10
r963: expose mask_level
2014-10-30 11:33:43 -04:00
76a15ea91b
r933: with bwa-postalt ready, drop option -g
2014-10-21 00:23:14 -04:00
a6b5a30dab
r930: use 3rd round seeding by default
...
This strategy is similar to the seeding heuristic used by LAST. When it is used
alone, it is not as accurate as the current seeding strategy at least for short
reads. However, it may do a better job for a long contig mapped to multiple ALT
contigs. This seeding strategy is also relatively cheap to perform.
2014-10-20 17:34:15 -04:00
bfd5e1840f
shm works on small files, but not large ones
...
I don't know why. SHMMAX, SHMALL and SHMMNI are large enough.
2014-10-15 15:44:06 -04:00
0a2cf98293
r876: optionally ignore idxbase.alt file
2014-09-27 23:21:50 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
c982443210
r854: improved the calculation of pa
...
and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
92bc6849a3
r844: added intra-species contig mapping mode
2014-09-16 10:53:07 -04:00
90518f11e3
r843: presetting for ONT 2d reads
...
Somewhat working for 1d reads, but not very well
2014-09-16 10:38:15 -04:00
4b6eeb34c8
r830: optionally fixed chunk size
2014-09-15 23:42:24 -04:00
5d26ab0ee3
r828: changed the default scoring for pacbio
2014-09-15 23:22:05 -04:00
35ac99b4f7
r815: optionally output ref fasta header
...
Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
b5cba257c1
r809: new strategy for the -a mode
2014-08-25 11:59:27 -04:00
08517ac09b
r764: changed -c in "-x pacbio" to 500
2014-05-13 12:53:24 -04:00
a35a6c2580
updated maual page
2014-05-12 12:52:16 -04:00
39a6cd5bb0
r762: cleanup for the new release; unfinished
...
It will take to make the documentation ready.
2014-05-11 15:15:44 -04:00
6ac8dd5840
r754: added command msg for -h
2014-05-06 16:15:14 -04:00
ce3c198245
r749: max_hits tunable on CMD; default to 5
2014-05-04 10:17:03 -04:00
11698fc4e5
r735: fixed a bug caused by merge
2014-04-30 13:12:43 -04:00
76bb49e01b
r729: halved band width; doubled patch band width
2014-04-24 16:06:01 -04:00
b92bbb47e5
Merge branch '0.7.7-softclip' into layout
...
Conflicts:
Makefile
bwamem.h
fastmap.c
main.c
2014-04-24 12:24:49 -04:00
8c12ec4a4b
r725: optionally disable hard clipping
...
as is reqested by the cancer group
2014-04-24 11:56:43 -04:00
00a07f61bf
r721: merge overlapping hits by default
2014-04-15 16:16:04 -04:00
4e22270eba
r718: merge alnregs overlapping on both query/ref
2014-04-14 17:01:17 -04:00
6d4a6debdc
r716: changed -x pbread
2014-04-14 16:04:29 -04:00
bbcabfe342
r707: change params for pacbio-to-pacbio
2014-04-10 21:53:52 -04:00
db58392e9b
dev-469: fixed wrong command line prompt
2014-04-09 13:20:04 -04:00
d766591c1e
dev-468: fixed a segfault caused by NULL
2014-04-08 22:11:36 -04:00
99f6f9a0d1
dev-467: limit the max #chains to extend
2014-04-08 21:45:49 -04:00
f12dfae772
dev-465: a new output format for read overlap
...
Also moved a few functions to bwamem_extra.c. File bwamem.c is becoming far too
long.
2014-04-08 16:29:36 -04:00
b45aeb87e1
dev-464: preset for pacbio read2read aln
2014-04-08 11:40:54 -04:00
172ba83241
dev-463: added option -x to change multiple params
...
I hate to copy-paste long command line options.
2014-04-07 11:29:36 -04:00
114901b005
dev-r462: refined setting for PacBio; weight flt
...
The recommended setting in the last commit is wrong. If we can extend a random
seed hit to the full length, we will force the read aligned through break
points, which is wrong. The new setting is better but it may lead to a small
fraction of fragmented alignments.
In addition, I added a filter on the minimum chain weight and tied
min_HSP_score to this filter. It doubles the mapping speed.
2014-04-04 17:01:04 -04:00
41f720dfa7
dev-461: added a heuristic for PacBio data
...
See the comment above mem_test_chain_sw() for details.
2014-04-04 16:05:41 -04:00
b3225581be
dev-458: simplified the smem iterator
...
simpler but less powful.
2014-04-03 15:23:48 -04:00
3efb7c0e91
r455: release bwa-0.7.8
2014-03-31 15:27:23 -04:00
127c00cc96
dev-454: wording change in command line prompt
2014-03-31 12:03:27 -04:00
b27bdf1ae0
dev-453: change of -A scales -TdBOELU
...
These paramemters are all proportional to -A.
2014-03-31 11:52:52 -04:00
b7076d9023
dev-r452: allow to specify insert size at cmd
...
This is also very useful for debugging.
2014-03-31 11:21:03 -04:00
Andreas Tille
John Marshall
José Manuel Abuín Mosquera
Heng Li