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Indexed stats estimation not reporting correct result on a 1000 genomes BAM file #1233

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cmdcolin opened this Issue Oct 12, 2018 · 1 comment

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cmdcolin commented Oct 12, 2018

The current indexed stats estimation seems to produce the wrong result on http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam from 1000 genomes. I don't believe there is any regression between @gmod/bam and older code

It reports number of features to be 40669

The full contents of the dummy bin look like this

fastDeclareClass {minv: fastDeclareClass, maxv: fastDeclareClass, bin: 37450}
bin: 37450
maxv: fastDeclareClass {block: 0, offset: 7247}
minv: fastDeclareClass {block: 44, offset: 40669}
__proto__: Object

Samtools idxstats produces the correct output

samtools idxstats http://s3.amazonaws.com/1000genomes/phase3/data/HG00096/alignment/HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam
1       249250621       0       0
2       243199373       0       0
3       198022430       0       0
4       191154276       0       0
5       180915260       0       0
6       171115067       0       0
7       159138663       0       0
8       146364022       0       0
9       141213431       0       0
10      135534747       0       0
11      135006516       0       0
12      133851895       0       0
13      115169878       0       0
14      107349540       0       0
15      102531392       0       0
16      90354753        0       0
17      81195210        0       0
18      78077248        0       0
19      59128983        0       0
20      63025520        2924253 7247
21      48129895        0       0
22      51304566        0       0
X       155270560       0       0
Y       59373566        0       0

@rbuels rbuels added the bug label Oct 12, 2018

@rbuels rbuels added this to the 1.15.5 milestone Oct 12, 2018

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cmdcolin commented Oct 12, 2018

This should be fixed in bam-js now. I'll make a PR for JBrowse to pull this in sometime shortly :)

@cmdcolin cmdcolin closed this Oct 13, 2018

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