<div dir="ltr"><span style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px">Morning</span><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px"><div>I'm just fiddling with the coverage mode and saw what looks like a 1/2 open issue, or maybe an assumption that bams are using 1/2 open coords.</div><div><br></div><div>Samtools show 2 reads starting at 10000:</div><div>```</div><div>$ samtools view test.bam chr1:1-10000</div><div>NB501627:84:HMJNWBGX2:3:22601:<wbr>21701:15135    121    chr1    10000    0    49S30M    =    100000    <wbr>AATAAATTATAGATTATATAAAAATTAATT<wbr>AATAATGCTTCCCCTATCCATAACCCTAAC<wbr>CCTAACCCTAACCCTAACC    //AE//////////EE////////////<wbr>E///E/////E/////A/////E//////<wbr>EEEEEAEEEEEEEEEEEAAAAA</div><div>NB501627:84:HMJNWBGX2:3:22601:<wbr>21701:15135    181    chr1    10000    0    *    =    100000    <wbr>AATATTAATTAATTATTATTTAATCGATAA<wbr>TATATTAATATTATTTAATCGTATTTAAAT<wbr>TGTTTGTGGTTGTGGGTGAG    EEEE/EEAAEEEE/<wbr>EEAEEEEEEEEEEEEEEEEEEEEEEEEEEE<wbr>EAEEEEEAE/<EEE/EEEEEEEEEA/<wbr>EEEEEA/AAA </div><div>```</div><div>Tags truncated for brevity.</div><div><br></div><div>Wiggletools shows none:</div><div>`$ wiggletools seek chr1 1 10000  coverage test.bam`</div><div><br></div><div>When extending to 10001, the coverage value only show 1, not 2?</div><div>```</div><div>$ wiggletools seek chr1 1 10001  coverage test.bam</div><div>fixedStep chrom=chr1 start=10000 step=1</div><div>1.000000</div><div>```</div><div><br></div><div>Can someone confirm what's going on here?</div></div><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px">Thanks</div><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px"><br></div><div style="font-family:roboto,"helvetica neue",helvetica,arial,sans-serif;font-size:12.8px">Nathan</div></div>