I understand that the -pc option of genomecov requires a BAM file that is name-sorted.
However, I am using bedtools version 2.31.0, and I encounter the following error when using a name-sorted BAM file with the -pc option:
Input error: Chromosome chr9 found in non-sequential lines. This suggests that the input file is not sorted correctly.
On the other hand, using a position-sorted BAM file does not produce any errors, and it seems to work fine.
Is this issue related to the bedtools version?
Additionally, does using a position-sorted BAM file instead of a name-sorted BAM file produce the same results when using the -pc option in this version?
I understand that the -pc option of genomecov requires a BAM file that is name-sorted. However, I am using bedtools version 2.31.0, and I encounter the following error when using a name-sorted BAM file with the -pc option: Input error: Chromosome chr9 found in non-sequential lines. This suggests that the input file is not sorted correctly.
On the other hand, using a position-sorted BAM file does not produce any errors, and it seems to work fine.
Is this issue related to the bedtools version? Additionally, does using a position-sorted BAM file instead of a name-sorted BAM file produce the same results when using the -pc option in this version?