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
Best
-Dominique
On Wed, Sep 25, 2013 at 7:27 PM, Lauren Oldfield <lmo14@pitt.edu> wrote:
> My question: How can I generate a pileup with an output of more than 8000
> hits per base? I was generating pileups using the SAM tools --> Generate
> pileup and do not see an option to change the settings for output. In
> mpileup there is a variable that looks correct, -D (Output per-sample read
> depth) , but I cannot figure out how to adjust it. I checked the box, Output
> per-sample read depth, under the advanced settings but the log file
> generated still says the max depth was 8000.
>
> The pileup files I generated look great but I would like to know what the
> true read depth is at the 8000 hit plateaus.
Hi Lauren,
Unfortunately this is a samtools design choice, 8000 is the
coverage limit hard coded in the source code itself (see files
bam_pileup.c and bam_plcmd.c), so at the very minimum it
would mean manually editing the samtools source and
recompiling samtools.
It would be best to ask about this on the samtools-help mailing
list (CC'd), as it may be more complicated than just editing a few
lines of the C code.
For the samtools folk - could this magic limit of 8000 be done
via a #define to make it clearer this is a special constant, and
give people just one place to change the code?
> Any help appreciated. I'm a little out of my depth here.
Ha ha, good pun.
Peter
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