3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
cfa7165036
cleanup index loading code
2013-02-23 16:10:48 -05:00
6ad5a3c086
removed color-space support
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which has been broken since 0.6.x
2013-02-12 10:21:17 -05:00
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
a1abfe9977
API: aln seems working
2012-04-07 00:23:01 -04:00
d33abf127f
check *.64.bwt first and then *.bwt
2012-03-29 14:45:00 -04:00
bdc953cad9
Tim's suggestion suffix file name with .64
2012-03-29 12:22:51 -04:00
dec584d50b
fixed a long-existing bug in trimming
2011-11-23 23:11:50 -05:00
2f3cdcd55b
bugfix: bwa-short MT does not work (by Peter)
2011-11-12 16:54:38 -05:00
098f44cd51
nothing
2011-10-20 16:26:14 -04:00
156852b1dd
no change
2011-10-20 16:15:16 -04:00
2d2db5d50f
aln seems working
2011-10-20 16:13:35 -04:00
db59a605d1
Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y
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In Casava 1.8 the fastq output changed. e.g.
@EAS139:136:FC706VJ:2:5:1000:12850 1:Y:18:ATCACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBCCCC?<A?BC?7@@???????DBBA@@@@A@@
The part after the space, treated as comment by bwa, contains the fields:
<read number>:<is filtered>:<control number>:<barcode sequence>
With `Y' Casava indicates that a sequence should be filtered. This patch
enables bwa, with an -Y flag, to filter these sequences.
Signed-off-by: Roel Kluin <roel.kluin@gmail.com>
2011-07-10 17:04:06 +02:00
8f115a8e00
Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa"
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This reverts commit 36cd4f9882
2011-07-10 16:40:42 +02:00
36cd4f9882
In Casava 1.8 the fastq output changed, the name had a space which bwa
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wasn't parsing correctly. This patch fixes that and enables bwa to filter
sequences marked by Casava, removing this tag from the output.
Signed-off-by: RoelKluin <roel.kluin@gmail.com>
2011-07-08 16:49:09 +02:00
243e735431
applied patches from Alec Wysoker
2011-05-04 09:46:50 -04:00
8d6b859bf8
speed up multi-threading
2011-04-07 17:26:08 -04:00
51d354cd28
Added barcode support
2011-01-15 15:35:39 -05:00
10721ca602
Added an option to accept Illumina 1.3+ fastq
2011-01-15 14:07:08 -05:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Rob Davies
Heng Li
Heng Li
Roel Kluin