shiquan

broken +1 compiler: gcc

The similar question has been reported here https://github.com/shiquan/bamdst/issues/3. I have added this requestion in my todo list. And I will close this issue after update.

now support, thanks to @biolxy

Sorry for the later reply. What aligner did you use? I think this difference comes from the aligner skip some reads in default. `samtools view $bam | wc -l `...

@ray1919 Can you try to use `samtools flagstat` to confirm this. There might be some different due to secondary alignments.

now support.

Sorry for the later reply. Did you fix this problem? The reads covered both the target region and the flank region will be count at each term. So at this...

I think the process has killed because out of memory. Try to split each chromosome into small pieces.

Try to divide the chromosome region into 1M pieces. If it's still not works, plz send your bed file to my email, I will check it. [email protected]

@xiucz make sure it should be at least 1bp for nearby regions. Because bamdst will merge the bed file before read counting. I didn't test the following command but it...