Is your feature request related to a problem? Please specify.
With samtools cat, we can now slice across CRAM files by container, using the syntax:
samtools cat -r "#:start-end" $cram
It would be nice to have a similar functionality for samtools faidx, in order to facilitate random access to a slice of FASTA/FASTQ records. This would be useful to facilitate e.g. chunked mapping of reads to a reference across multiple jobs, without first splitting a FASTA file into chunks.
Describe the solution you would like.
Perhaps a similar syntax to samtools cat? Extend the region definition so that regions starting with # returns a slice of the fastX file? e.g.
samtools faidx $reads.fq.gz #:0-100000
or
echo #:0-100000 > regions.list
samtools faidx -r regions.list $reads.fq.gz
Is your feature request related to a problem? Please specify.
With
samtools cat, we can now slice across CRAM files by container, using the syntax:It would be nice to have a similar functionality for
samtools faidx, in order to facilitate random access to a slice of FASTA/FASTQ records. This would be useful to facilitate e.g. chunked mapping of reads to a reference across multiple jobs, without first splitting a FASTA file into chunks.Describe the solution you would like.
Perhaps a similar syntax to
samtools cat? Extend the region definition so that regions starting with#returns a slice of the fastX file? e.g.or