1) on bam-file with more than 1000 reads paired end (using -profile test),
2) on bam-file with less than 1000 reads all of which are paired, and
3) on bam-file with less than 1000 reads including a couple of reads that are not paired.
As far as I understand, in the instruction samtools view $reference $input -@$task.cpus | head -n1000, samtools will read/parse at most 1000 lines from the input-bam, and that is what we want. We don't want samtools to spend time reading all reads from huge bam-files.
Fixing #22.
Tested manually:
1) on bam-file with more than 1000 reads paired end (using
-profile test
), 2) on bam-file with less than 1000 reads all of which are paired, and 3) on bam-file with less than 1000 reads including a couple of reads that are not paired.As far as I understand, in the instruction
samtools view $reference $input -@$task.cpus | head -n1000
, samtools will read/parse at most 1000 lines from the input-bam, and that is what we want. We don't want samtools to spend time reading all reads from huge bam-files.