Hi,
Can you try using -M option, together with -L?
samtools view -ML tmp.bed -X -r 364940 my.bam my.bai
From: Keiran Raine <k...@sanger.ac.uk>
Sent: 24 September 2020 11:11
To: samtools-help@lists.sourceforge.net
Subject: [Samtools-help] samtools view -L vs location args [EXT]
Hi,
Are there any plans to make the -L option perform more efficiently? Using the
file based approach for even 1 loci appears to result in a full scan of the BAM:
$ time samtools view -X -r 364940 my.bam my.bam.bai chr1:65419886-65419886 >
/dev/null
real 0m0.076s
user 0m0.042s
sys 0m0.031s
$ time samtools view -L tmp.bed -X -r 364940 my.bam my.bai > /dev/null
^C # gave up as it's a big file
real 3m42.755s
user 3m41.225s
sys 0m1.392s
$ cat tmp.bed
chr1 65419885 65419886
I understand that it may be beneficial to have the ability to switch between
"full scan" and random access but it would be useful if this was able to be
specified by the user.
If I'm missing some option please let me know, otherwise happy to raise an
issue about this,
Thanks.
Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute
k...@sanger.ac.uk<mailto:k...@sanger.ac.uk>
Office: D3-19
Ext: 4983
Please note that due to childcare requirements due to covid restrictions I am
generally not available after 4pm.
-- The Wellcome Sanger Institute is operated by Genome Research Limited, a
charity registered in England with number 1021457 and a company registered in
England with number 2742969, whose registered office is 215 Euston Road,
London, NW1 2BE.
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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