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Description
Region strings passed to --chrom
can be of the format ref_id:start-end
to only consider part of a reference sequence. However, reference sequences sometimes have :
in their sequence name (e.g. if they were created with samtools faidx
. In this case, mosdepth
fails with chromosome name ... not found
if the whole reference name is provided (see example below).
Example:
$ samtools view -h example.bam
@HD VN:1.6 SO:unsorted GO:query
@SQ SN:seq:1-100 LN:100
@PG ID:samtools PN:samtools VN:1.19 CL:samtools view -h example.bam
read 0 seq:1-100 1 4 100M * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * NM:i:0 ms:i:200 AS:i:200 nn:i:0 tp:A:P cm:i:85 s1:i:100 s2:i:98 de:f:0 rl:i:0
$ mosdepth test example.bam --chrom seq:1-100
[mosdepth] chromosome seq not found
In contrast, samtools
commands work with sequence IDs that contain colons (see example below).
samtools
example:
$ cat ref.fa
>seq:1-100
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
$ samtools faidx ref.fa seq:1-100
>seq:1-100
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
$ samtools faidx ref.fa seq:1-100:50-60
>seq:1-100:50-60
AAAAAAAAAAA
Could mosdepth
be adapted to do the same?
Many thanks!
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