Hi Lauren, You could try to apply the following patch which sets the limit from 8.000 to 1.000.000:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=671524 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 Thu, Sep 26, 2013 at 6:14 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Wed, Sep 25, 2013 at 7:27 PM, Lauren Oldfield <lm...@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 > > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60133471&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > samtools-h...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help >
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