fast-bwa

Commit Graph

Author	SHA1	Message	Date
Heng Li	5a0b32bfd2	updated to the latest kseq.h	2013-02-06 14:38:40 -05:00
Heng Li	717959e819	fixed a minor issue in trimming	2011-11-24 10:39:41 -05:00
Heng Li	dec584d50b	fixed a long-existing bug in trimming	2011-11-23 23:11:50 -05:00
Roel Kluin	db59a605d1	Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y 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
Roel Kluin	8f115a8e00	Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa" This reverts commit `36cd4f9882`. The comment shouldn't be included in the sequence name.	2011-07-10 16:40:42 +02:00
RoelKluin	36cd4f9882	In Casava 1.8 the fastq output changed, the name had a space which bwa 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
Heng Li	a74523a68d	increase maximum barcode length limit to 63bp	2011-06-09 17:17:13 -04:00
Heng Li	51d354cd28	Added barcode support	2011-01-15 15:35:39 -05:00
Heng Li	10721ca602	Added an option to accept Illumina 1.3+ fastq	2011-01-15 14:07:08 -05:00
Heng Li	007c3eb75d	Imported from my local bwa repository, the master repository.	2011-01-13 20:52:12 -05:00

10 Commits (64d92d26dfe712be2f28d58ea1be6cdfea881d6f)