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Id: 66209
Status: new
Priority: 0/
Queue: Bio-SamTools

Owner: Nobody in particular
Requestors: Yi-Shiou.Chen [...]

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Fixed in: (no value)

Subject: Suggested change to coverage_from_pileup_fun in Sam.xs
Date: Sat, 26 Feb 2011 13:08:26 -0800
To: "bug-Bio-SamTools [...]" <bug-Bio-SamTools [...]>
From: Yi-Shiou Chen <Yi-Shiou.Chen [...]>
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Suggest to change coverage_from_pileup_fun in Sam.xs as below so that coverage will not count reads that actually skip the region. int coverage_from_pileup_fun (uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) { coverage_graph_ptr cgp; int bin; int toSkip; int i; const bam_pileup1_t* r; cgp = (coverage_graph_ptr) data; cgp->reads += n; if (n > 0 && pos >= cgp->start && pos <= cgp->end) { toSkip = 0; for(i = 0; i < n; i++) { r = pl + i; if(r->is_refskip == 1 || r->is_del == 1) toSkip++; } n-=toSkip; bin = (pos-cgp->start)/cgp->width; cgp->bin[bin] += n; } return 0; } This is a fix to bug #66138, which occurs when using the latest samtools release. Thanks, Yi-Shiou Chen Accelrys

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