ataqc
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kundajelab
Hi I noticed in line 430. when get the count of bam, you shift_width to center the read on the cut site ``` bam_array = bam.array(tss_ext, bins=bins, shift_width = -read_len/2,...
Is the QC already working with mm10? In the run_ataqc.sh script I saw the comment that so far only hg19 is working. When I try to run the pipeline with...
If I'm not mistaken, the scritpt `run_ataqc.py` is broken due to a change of API in `samtools sort`, notably lines [522](https://github.com/kundajelab/ataqc/blob/d5b65453e25cc6481692cd46e8cfeae8a61850b0/run_ataqc.py#L522) and [524](https://github.com/kundajelab/ataqc/blob/d5b65453e25cc6481692cd46e8cfeae8a61850b0/run_ataqc.py#L524). See [samtools 1.3 release](https://github.com/samtools/samtools/releases/tag/1.3): >The obsolete samtools...
