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2833 Commits (cc3c18d3e189918e604d5f70fdc2dc74fef28a1c)

Author SHA1 Message Date
aaron cc3c18d3e1 a small dbsnp file for Tribble testing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2853 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:12:55 +00:00
ebanks 7669eaaeb3 Optimizations to the cleaner algorithm; reduce total runtime by almost 20%. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2852 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:10:56 +00:00
aaron 8fd3351971 adding a stripped down Tribble library for the start of integration 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2851 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 21:29:25 +00:00
ebanks 79ab7affda - Change sortOnDisk option to sortInMemory 
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 20:52:57 +00:00
ebanks 2520889cb3 Check for bad intervals and don't emit them 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 21:42:36 +00:00
kiran f859e14cc7 Allow no-call alleles to propagate through to the MAF file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2848 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:46:16 +00:00
kiran 217deb9809 Changed the INFO field delimiter from a comma to a semicolon 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2847 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:44:57 +00:00
aaron 653f70efa2 added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2846 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:35:35 +00:00
chartl f02e94ab6f Eliminate the rescale factor -- heatmap automatically normalizes the data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2845 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 16:34:33 +00:00
chartl 0e4b5ad9c6 Check to ensure sample status is "Complete" before writing out the bam file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2844 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 15:36:42 +00:00
chartl 37fa1bf0cc Added heatmap function 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2843 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 15:12:54 +00:00
chartl 01af3d0663 Update an error message :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2842 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 23:24:06 +00:00
chartl 951b7a2433 First of what will be an increasingly useful set of tools, compiled into one command-line runnable library -- the goal is to have one plotting library that's callable because of limitations on the number of files you can package with a GenePattern module. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2841 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 16:51:47 +00:00
jmaguire 81313d9452 added class VCFMerge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2840 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 14:41:50 +00:00
jmaguire 0ef50bcae7 - update to match recent changes in the VCF parser 
- compute Het Error Rate in VCFConcordance
- changes to the frequency-specific optimizer




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2839 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-15 14:27:01 +00:00
depristo 8072e9aed5 should never commit without running intergration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 23:42:37 +00:00
depristo a1a3d5fcb0 Support for reading in table of rsIDs -> dbSNP builds to back generate a dbSNP build X from a single file. Very useful indeed. dbSNP -> VC now captures the rsID in the context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2837 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 22:40:55 +00:00
kcibul 28f24ca2ae made some private member/methods protected to allow for subclassing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2836 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 21:16:00 +00:00
hanna 232d884578 Got back most of the performance lost when I fixed the dropped reads problem. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2835 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 19:59:56 +00:00
chartl 04a2784bf7 Initial commit of tools under development for data QC through firehose. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2834 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 19:13:24 +00:00
hanna 77af5822d4 Correcting my incomplete understanding of how the BAM file index actually works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2833 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 16:15:19 +00:00
depristo 5f74fffa02 Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2832 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:26:52 +00:00
depristo 197dd540b5 added root GATKData variable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2831 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:25:34 +00:00
ebanks c6f6948f9d Haiku: 
Eric is a fool.
Matt found his really dumb bug.
Eric is humbled.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2830 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 04:51:56 +00:00
kiran d4e4120ca1 Some useful changes that I've had laying around for a while - deletes files from failed runs, automatically adds a memory limit to java commands where one isn't specified, and touches files on the local machine after command completion to get around the problem with the times not being perfectly synchronized across LSF nodes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2829 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 00:18:34 +00:00
rpoplin ecebf0bc62 Bug fix for null pointer exception in AnalyzeAnnotations if -name argument isn't specified 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2828 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 18:39:26 +00:00
mmelgar ad608d0e9d Cleaned up documentation on SecondaryBaseTransitionTableWalker and added Read Group and Allele Balance to the info. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2827 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 17:20:35 +00:00
hanna 34e566c90d Fixed bug where new sharding system wasn't grabbing the reads that start at the end of a bin. Caused by what I currently believe to be a bug in Picard -- will verify with Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2826 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 17:00:04 +00:00
ebanks 96fee7cf7a Disabling input of known indels for use as alternate consenses. When we get rods in a read traversal, it will be trivial to hook it into the cleaner (the code is already there). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2825 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 15:52:21 +00:00
chartl e491b42951 Dumb little script that grabs Picard metrics (alignment, hybrid selection, insert size) from picard_aggregation given the path to the bam file; zips them up, and spits them out; for use with Firehose 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2824 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 14:09:30 +00:00
ebanks a4a2c9b172 Deal with bad input; also N-way out isn't default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2823 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-11 03:44:56 +00:00
hanna dc885ba386 Fix for some correctness bugs found during early performance testing, phase 1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2822 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 22:32:25 +00:00
chartl 60f05379a7 fix typo. Check explicitly that fingerprint files exist. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2821 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 21:29:54 +00:00
chartl d16a1b5645 Simple python script for generating a firehose-parseable text file from MS-Dos formatted TSV spreadsheets (of the type that we get from project management). Will be deprecated in a few weeks with the advent of direct BSP ID entries, but useful until then. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2820 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 20:25:40 +00:00
depristo c66861746a improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 16:12:29 +00:00
rpoplin 3de72daa88 Removing an accidently added import statement. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2818 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:54:24 +00:00
rpoplin 0b1e243a7b CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:52:20 +00:00
ebanks 6652b992f7 The new cleaner can now use known indels to create alternate consenses for cleaning. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2816 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 04:39:15 +00:00
hanna 0250338ce7 Basic use cases for merging BAM files with the new sharding system work. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2815 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 22:14:37 +00:00
depristo 934d4b93a2 VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 19:02:25 +00:00
andrewk 369cc50802 Added playground walker that does a basic concordance check between two VCF files - an eval and a truth file - across all samples in the eval file. Produces per-sample, per-locus debug info and simple concordance stats. This is not meant to be extended, but rather used for validating the HapMap to VCF conversion in preparation for retiring GFF-based HapMap data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2813 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 02:41:18 +00:00
depristo 94f892ad42 VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:22:05 +00:00
depristo 457568485a simple Beagle input ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2811 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:21:04 +00:00
hanna 57b8c9a53c Supporting infrastructure for merging SAM files. Not yet integrated into the datasource. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2810 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 23:59:38 +00:00
kshakir fc810a1800 Updated VCF Reader to parse VCFs according to the VCFv3.3 spec. Column headers are tab separated since sample names might have spaces. 
Updated test files in /humgen/gsa-scr1/GATK_Data/Validation_Data/*.vcf to remove spaces except for when they are supposed to be in the sample name.
Added @Test before VCFReaderTest.testHeaderNoRecords()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2809 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 22:55:59 +00:00
chartl 935e76daa1 Minor changes to oneoff walkers. PlinkRod altered but still commented. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2808 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 18:49:56 +00:00
hanna 21369869b7 Extend regex that supports every 'word' character to use any printable character except ':'. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2807 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 03:29:55 +00:00
ebanks 4fe851a83d Optimization: don't keep scoring an alternate consensus if it's already worse than the best alt seen so far. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2806 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 05:06:32 +00:00
ebanks ca1917507f Various improvements and fixes: 
In indel cleaner:

1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.

2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header.  This entailed some reworking of the datasources code.

3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses.  Not done yet.

In UG: fix bug in beagle output for Jared.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 04:21:04 +00:00
kshakir 57a168c0db Added a header crediting the python script as a source. Looping over an arbitrary number of headers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2804 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 03:38:30 +00:00