Hi,
The tabix is able to retrieve the many regions listed in a file by using
the -R option while "samtools faidx" can only extract the regions specified
on the command region arguments and there is no "-R" option as in tabix.
I have looked at the htslib and found that this feature can be implemented
in C by calling the API. I'm wondering if we can have the "-R" option for
the command "samtools faidx".
While I am at it, the -R for tabix may list many rows of the data for one
region specified by the -R option. Will it be possible to have the first
column to be the region index for the each line of the output (or the
region info as the sequence name in the output samtools faidx) so that we
know which regions are exactly queried for that line.
Again, this feature can be implemented using the htslib API, but these
implemented features will be a lot of help for the maintenance and for the
people who don't know C program.
Thanks,
Yongchao
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