Package: samtools
Version: 0.1.18-1
samtools depth sets a cap of 8000 for coverage. It becomes an issue
when used to calculate depth for targeted sequencing applications.
Attached patch increases the threshold to 1 million.
Is this safe to apply?
Thanks
-Dominique
Index: bam2depth.c
===================================================================
--- bam2depth.c (revision 995)
+++ bam2depth.c (working copy)
@@ -80,6 +80,7 @@
// the core multi-pileup loop
mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
+ bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M
n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of
covering reads from the i-th BAM
plp = calloc(n, sizeof(void*)); // plp[i] points to the array of
covering reads (internal in mplp)
while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to
the next covered position
Patch taken from here:
http://sourceforge.net/mailarchive/message.php?msg_id=28166483
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