Bio::DB::Sam->max_pileup_cnt([$new_cnt])

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Bio::DB::Sam->max_pileup_cnt([$new_cnt])

Jim Hu
How can I set this in gbrowse2?  A user is complaining that their peaks are cut off.  

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Bio::DB::Sam->max_pileup_cnt([$new_cnt])

Timothy Parnell
Hi Jim,

I don't think you can. You can try putting it in the db_args argument when setting up the Bam database, but I don't think it'll get recognized.

As a workaround, have you tried converting the coverage to a wig or bigWig file to get around it?

Tim


On Nov 28, 2013, at 9:12 AM, Jim Hu <[hidden email]<mailto:[hidden email]>> wrote:

How can I set this in gbrowse2?  A user is complaining that their peaks are cut off.

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Bio::DB::Sam->max_pileup_cnt([$new_cnt])

Jim Hu
Hi Tim,

It's actually a bit worse than what I explained.  I need to set it so a user's custom track will not be cut off. One of the things about working with bacterial and phage is that we get ridiculous coverage from the same number of illumina runs.

So... I guess I need to figure out a way to put a warning up in the custom upload section that points to a tutorial about how to make a wig or bw to upload instead of or in addition to the bam.  I hope they do both; it's nice to be able to get the reads in addition to the counts.  For example, we have some ribosome profiling data from our users where a question came up about the distribution of the protected fragment sizes.

Jim


On Dec 2, 2013, at 11:08 AM, Timothy Parnell wrote:

Hi Jim,

I don't think you can. You can try putting it in the db_args argument when setting up the Bam database, but I don't think it'll get recognized.

As a workaround, have you tried converting the coverage to a wig or bigWig file to get around it?

Tim


On Nov 28, 2013, at 9:12 AM, Jim Hu <[hidden email]<[hidden email]>> wrote:

How can I set this in gbrowse2?  A user is complaining that their peaks are cut off.

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Bio::DB::Sam->max_pileup_cnt([$new_cnt])

Keiran Raine
Hi Jim,

We saw this issue when the max_pileup_cnt was introduced to samtools.  As we had code that wasn't setting it we actually patched out samtools (C-library) to set this to INT_MAX.  Just make sure you only do this to the copy of samtools used by GBrowse.

I put a patch request into the Bio::DB::Sam bug tracker for this to always be set high when running bamToGBrowse.pl via CPAN, but I don't think it's been picked up… I've just replicated it across to the github tracker.

--- samtools-0.1.17/bam_pileup.c.orig   2010-11-22 03:17:02.000000000 +0000
+++ samtools-0.1.17/bam_pileup.c        2011-08-03 16:39:10.000000000 +0100
@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <ctype.h>
 #include <assert.h>
+#include <limits.h>
 #include "sam.h"
 
 typedef struct {
@@ -169,7 +170,7 @@
        iter->dummy = mp_alloc(iter->mp);
        iter->max_tid = iter->max_pos = -1;
        iter->flag_mask = BAM_DEF_MASK;
-       iter->maxcnt = 8000;
+       iter->maxcnt = INT_MAX;
        if (func) {
                iter->func = func;
                iter->data = data;

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Dec 2013, at 21:03, Jim Hu <[hidden email]> wrote:

Hi Tim,

It's actually a bit worse than what I explained.  I need to set it so a user's custom track will not be cut off. One of the things about working with bacterial and phage is that we get ridiculous coverage from the same number of illumina runs.

So... I guess I need to figure out a way to put a warning up in the custom upload section that points to a tutorial about how to make a wig or bw to upload instead of or in addition to the bam.  I hope they do both; it's nice to be able to get the reads in addition to the counts.  For example, we have some ribosome profiling data from our users where a question came up about the distribution of the protected fragment sizes.

Jim


On Dec 2, 2013, at 11:08 AM, Timothy Parnell wrote:

Hi Jim,

I don't think you can. You can try putting it in the db_args argument when setting up the Bam database, but I don't think it'll get recognized.

As a workaround, have you tried converting the coverage to a wig or bigWig file to get around it?

Tim


On Nov 28, 2013, at 9:12 AM, Jim Hu <[hidden email]<[hidden email]>> wrote:

How can I set this in gbrowse2?  A user is complaining that their peaks are cut off.

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Sponsored by Intel(R) XDK
Develop, test and display web and hybrid apps with a single code base.
Download it for free now!
http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse