[PATCH] allow bwa to parse Casava 1.8 fastqs and filterer flagged#1
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RoelKluin wants to merge 3 commits into
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[PATCH] allow bwa to parse Casava 1.8 fastqs and filterer flagged#1RoelKluin wants to merge 3 commits into
RoelKluin wants to merge 3 commits into
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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>
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Thanks. Nonetheless, you should not modify kseq.h. By convention, a FASTA name should not contain any space. Anything beyond space is comment. Allowing space in sequence names as is in the modified kseq.h will cause problems to other input sequences. If you want to get the string after space in the fasta/q header lines, you should check "kseq_t::comment". Could you help to modify using "kseq_t::comment" without touching kseq.h? Thanks. |
…which bwa" This reverts commit 36cd4f9. The comment shouldn't be included in the sequence name.
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>
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ksprintf is inline, to avoid collision with htslib
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lh3#5 real) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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In Casava 1.8 the fastq output changed, the name has a space which bwa
wasn't parsing correctly. This patch fixes it and enables bwa to filter
sequences marked :Y: by Casava. The tag is removed from the output.
Signed-off-by: RoelKluin roel.kluin@gmail.com