Issue with new samtools 1.0 index and idxstats

[swbarnes2]

When using samtools 1.19, I would index my .bam, and use idxstatst to make a file of read counts per sequence in my reference, and the unmapped reads would be at the bottom of the list.

The line would look like

* 0 0 1027820

To show 1027820 reads did not align

When using samtools 1.0 to index, now, the idxstats file always claims there is exactly 1 read that mapped to nothing, which is clearly wrong.

Can anyone else replicate this? This can't be the desired behavior, can it?

[dpryan]

I just tested on an old BAM file (reindexed and ran idxstats) and got 0, as appropriate. Perhaps this only happens if there are unmapped reads in the file? I should note that you should ensure that both htslib and samtools are on the 1.0 tag release. When I just recloned them (just to ensure that any local changes weren't in there) I couldn't even compile samtools since the most current commit breaks compilation with the version of htslib I had from earlier in the day.

[swbarnes2]

I went into the htslib-1.0 folder of my samtools 1.0 folder, and "make" seems to finish without errors, but samtools 1.0 still does the same thing: idxstats run from the v 1.0 indexing shows only 1 unmapped read. Rebuilding the index with 0.1.19 and rerunning idxstats shows the correct number.

[dariober]

Can anyone else replicate this? This can't be the desired behavior, can it?

I just upgraded to samtools-1.0.

Indeed the same happens to me:

samtools --version
samtools 1.0
Using htslib 1.0
Copyright (C) 2014 Genome Research Ltd.

samtools index fk042_F5_14_CHEM1.bam
samtools idxstats fk042_F5_14_CHEM1.bam | tail -n1
*	0	0	1

## Now with samtools 0.18.0:
~/applications/samtools/samtools-0.1.18/samtools index fk042_F5_14_CHEM1.bam
samtools idxstats fk042_F5_14_CHEM1.bam | tail -n1
*	0	0	8882

[dpryan]

@dariober: In fact this is the issue I alluded to over on biostars :P

It turns out that this only happens if there are unmapped read in the BAM file (otherwise, it correctly reports 0).

[dpryan]

I've submitted a bug report.

[swbarnes2]

I've submitted a bug report.

Thank you. I didn't want to do that until I had some confirmation that other people were seeing the problem.

[dpryan]

I created a pull request to fix this.

[dariober]

I created a pull request to fix this.

Thanks a lot for taking care of this issue. Here's my comment to your post on github:

I'm quite keen on querying the index to get the number of unmapped reads, so I favour the second solution. (With the disclaimer the I'm not the one going to fix it though!)