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基于bwa，做一些优化，注释
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Heng Li 7babb54e4c drop smem based mapping algorithm 
While we can compute smems very efficiently, there is still a long way to get
the alignment. On simulated data, this smem-based algorithm is 4X faster than
bwasw and twice as fast as bowtie2, but the accuracy is far lower than bwasw
and even lower than bowtie2 in the high-mapQ range. I am kind of sure that if
we continue to increase the mapping accuracy, the speed will approach to bwasw,
if not slower.

Smem-based mapping algorithm is still interesting, but given that I am short of
time, I will not explore it further.
 		2011-10-27 10:56:09 -04:00
bwt_gen move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
.gitignore Added barcode support 2011-01-15 15:35:39 -05:00
COPYING Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
ChangeLog Update to the latest modfication 0.5.9rc1-2. Update ChangeLog 2011-01-13 20:54:10 -05:00
Makefile forward-backward search seems working 2011-10-25 12:31:36 -04:00
NEWS Release bwa-0.5.9 (r16) 2011-01-24 22:00:24 -05:00
QSufSort.c move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
QSufSort.h move bwt_gen/* to the root directory 2011-10-20 11:56:24 -04:00
README Release bwa-0.5.9 (r16) 2011-01-24 22:00:24 -05:00
bamlite.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bamlite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bntseq.c concatenate for-rev sequences in the end 2011-10-25 11:22:08 -04:00
bntseq.h fixed a minor issue about +/-1 2011-10-25 13:00:41 -04:00
bwa.1 updated revision number 2011-10-24 14:14:42 -04:00
bwape.c bugfix: integer overflow and strand error in sampe 2011-10-24 17:07:12 -04:00
bwase.c fixed a minor issue about +/-1 2011-10-25 13:00:41 -04:00
bwase.h PE seems working; more testing needed 2011-10-20 17:45:41 -04:00
bwaseqio.c Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y 2011-07-10 17:04:06 +02:00
bwt.c forward-backward search seems working 2011-10-25 12:31:36 -04:00
bwt.h forward-backward search seems working 2011-10-25 12:31:36 -04:00
bwt_gen.c print msg to stderr; output more in fastmap 2011-10-25 15:06:13 -04:00
bwt_lite.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwt_lite.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtaln.c nothing 2011-10-20 16:26:14 -04:00
bwtaln.h bugfix: integer overflow and strand error in sampe 2011-10-24 17:07:12 -04:00
bwtgap.c aln seems working 2011-10-20 16:13:35 -04:00
bwtgap.h aln seems working 2011-10-20 16:13:35 -04:00
bwtindex.c use forward-only pac to reduce memory 2011-10-21 12:03:14 -04:00
bwtio.c make changes to bwt.c 2011-10-19 17:42:42 -04:00
bwtmisc.c removed reverse pac; bwa is not working right now 2011-10-20 12:09:35 -04:00
bwtsw2.h not segfault immediately; but buggy 2011-10-24 09:36:52 -04:00
bwtsw2_aux.c fixed a potential int overflow 2011-10-24 14:22:39 -04:00
bwtsw2_chain.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
bwtsw2_core.c concatenate for-rev sequences in the end 2011-10-25 11:22:08 -04:00
bwtsw2_main.c this is better; but still buggy 2011-10-24 11:50:11 -04:00
cs2nt.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
fastmap.c drop smem based mapping algorithm 2011-10-27 10:56:09 -04:00
is.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
khash.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kseq.h Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa" 2011-07-10 16:40:42 +02:00
ksort.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kstring.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
kvec.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
main.c drop smem based mapping algorithm 2011-10-27 10:56:09 -04:00
main.h added bidirectional bwt; seems buggy 2011-10-25 00:22:28 -04:00
qualfa2fq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
simple_dp.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
solid2fastq.pl Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.c Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
stdaln.h Imported from my local bwa repository, the master repository. 2011-01-13 20:52:12 -05:00
utils.c applied patches from Alec Wysoker 2011-05-04 09:46:50 -04:00
utils.h applied patches from Alec Wysoker 2011-05-04 09:46:50 -04:00
xa2multi.pl Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment 2011-09-07 14:31:28 +02:00

README 

Released packages can be downloaded from SourceForge.net:

  http://sourceforge.net/projects/bio-bwa/files/

Introduction and FAQ are available at:

  http://bio-bwa.sourceforge.net

Manual page at:

  http://bio-bwa.sourceforge.net/bwa.shtml

Mailing list:

  bio-bwa-help@lists.sourceforge.net

To sign up:

  http://sourceforge.net/mail/?group_id=276243

Publications (Open Access):

  http://www.ncbi.nlm.nih.gov/pubmed/20080505
  http://www.ncbi.nlm.nih.gov/pubmed/19451168

Incomplete list of citations (via HubMed.org):

  http://www.hubmed.org/references.cgi?uids=20080505
  http://www.hubmed.org/references.cgi?uids=19451168