b89b9adb2c
misc code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2190 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 21:16:00 +00:00
e793e62fc9
minor code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2189 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:57:20 +00:00
4969cb1957
CountCovariates uses new optimized ReadBackedPileup. It also smarter about re-doing calculations for the dnsnp variation rate sanity check.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2188 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:35:40 +00:00
add2fa7ab4
more use of new ReadBackedPileup optimizations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2187 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:04:01 +00:00
f5fe28cc28
Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2186 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:02:25 +00:00
817e2cb8c5
Recalibrator makes use of the new GATKSAMRecord wrapper and now no longer has to hash the SAMRecord. Covariate's getValue method signature has changed to take the SAMRecord instead of the ReadHashDatum. ReadHashDatum removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2185 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 19:59:17 +00:00
e9a8156cfb
Use new optimized ReadBackedPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 18:17:18 +00:00
d8146ab23d
Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2183 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:55:23 +00:00
a184d28ce9
Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
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I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:39:29 +00:00
d5cda76c8b
A new subversion repository for matlab scripts, so they don't go away in case of catastrophic Yang failure.
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Might be useful if you want to learn matlab or make use of matlab scripts. It does have some advantages over R (and some disadvantages as well)
This script loads data from the FHS directory listing the average DoC per exon per gene per pool and makes a gene-by-gene box plot of the resulting data, broken up between pilot and production. It will also automatically save the resulting figures if you un-comment two lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2181 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 16:25:07 +00:00
af22ca1b47
Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 01:39:01 +00:00
2ea93385be
Better support for comparison to truth. Now emits FP rates for each covariate if a truth file is provided. Also now writes out a detailed recal.log file that can be parsed directly into R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2179 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 22:20:40 +00:00
662bbbd53b
Awful stupid bug. This will use up one of my bad code offsets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2178 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:09:33 +00:00
fa2d564f2c
And the compulsory one-second-later fix -- better handling of arguments (e.g. for callng from outside of /trunk/python/)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2177 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:02:43 +00:00
45673d7851
A quick and dirty script that, given a list of input VCF files, will output a new VCF file which looks identical to the first VCF file of the input list, except that the info field has been updated to reflect the union of all the INFO annotations across the VCF files
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Note: this is primarily for use with two files with mostly disjoint annotations. It views "SB=2.5" as a different info field than "SB=2.2" and so will output as info "SB=2.5;SB=2.2". That is, it compares the full field string, rather than only the field name.
Usage:
./mergeVCFInfoFields I=[comma-delimited list of files] O=[output file]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2176 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 20:01:29 +00:00
27651d8dc2
Oops. numReads is now called size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2175 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:59:17 +00:00
21744e024b
Quick walker that determines % of bases covered at (user - defined depth)x . I've been maintaining it in my directories alone, but now that i've accidentally deleted it twice, into playground it goes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:51:19 +00:00
3300ca906a
An iterator for Eric to use when injecting his new wrapping reads -- a stopgap solution for getting additional caching
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functionality into a SAMRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2173 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 22:25:52 +00:00
26db15be5c
Added SingleReadGroupFilter to only use reads from a specific read group, filtering out all others.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2172 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 20:33:59 +00:00
91f5672a32
misc cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2171 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 19:56:20 +00:00
d1298dda13
Encapsulated the sections of code that were shared by the two Recalibration walkers. This includes both the shared command line arguments and the section of code in the map methods which pull out data from the SAMRecord and stuff it into the ReadHashDatum. Command line arguments are now passed to the Covariates using a new initialize method that all Covariates must implement. Updated the dbsnp sanity check warning message to be less cryptic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2170 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 19:54:10 +00:00
75b61a3663
Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2169 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 23:30:39 +00:00
65da04ca85
Now uses the theoretically correct relationship between SNP FP and TP ratios for Illumina data. maxQ score for a snp is now 60
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2168 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 22:08:12 +00:00
49f020b0b9
Add to svn:ignore
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2167 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 21:42:40 +00:00
ac1b289d55
Add tile to ReadHashDatum, and implement TileCovariate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2166 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 21:41:42 +00:00
db40e28e54
ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2165 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 20:54:44 +00:00
b44363d20a
Removed silly casts from Integer to int.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2164 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:59:21 +00:00
84921b18ed
Push version number of picard-private-parts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2163 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:28:57 +00:00
5f2801e015
Push version number of picard-private-parts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2162 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:28:42 +00:00
d563f4bd2c
Add IlluminaUtil to picard-private.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2161 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:25:21 +00:00
d0f673f0c0
Use Math.abs so we don't get (inconsistent) -0's
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2160 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:08:34 +00:00
fe8809d12a
Added Covariate classes to the Early Access binary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2159 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 18:59:21 +00:00
e8bb88e33d
Updated package for early access
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2158 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 18:08:12 +00:00
6ff8526592
Added arguments to the recalibration walkers so the user can specify the default read group id and platform to use when a read has no read group. There are also options to force every read group and every platform to be the specified values. Added integration tests that use a bam file with no read groups. Added comments to all the covariates to explain what each of the methods in the Covariate interface are used for.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2157 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 15:41:12 +00:00
cfbd9332b0
small cleanups for the GATK paper genotyper; switched to the managed output system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2156 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 08:04:13 +00:00
e1e5b35b19
Don't have the spanning deletions argument be a hard cutoff, but instead be a percentage of the reads in the pileup. Default is now 5% of reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2155 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 04:54:44 +00:00
03342c1fdd
Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 03:51:41 +00:00
2cb3e53b0b
Verbose mode shouldn't be printing out 'NaN's and 'Infinity's
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2153 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 22:01:00 +00:00
c9ff5f209c
Added a CountCovariates integration test that uses a vcf file as the list of variant sites to skip over instead of the usual dbSNP rod.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2152 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:51:38 +00:00
3484f652e7
1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info.
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2. Killed OnOffGenoype
3. SpanningDeletions is now SpanningDeletionFraction
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:47:20 +00:00
e05cb346f3
GenotypeLocusData now extends Variation.
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Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs).
Technically, VCF records can be indels now.
More changes coming
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:07:55 +00:00
8b30279edc
style update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2149 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 20:56:31 +00:00
dffa46b380
BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2148 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 20:53:57 +00:00
8fbc0c8473
fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 19:19:47 +00:00
3fca23cd16
Added a stub treeReduce function for debugging multi-threaded execution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2146 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:51:19 +00:00
277e6d6b32
Further optimizations of TableRecalibration. This completes my goal of having the only math done in the map function be addition, subtraction and rounding the quality score to an integer. Everything else has been moved to the initialize method and only done once.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2145 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:21:57 +00:00
e4546f802c
Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency. Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points. Outputs R parseable file that has all data in lists and then does some basic plotting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2144 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:12:34 +00:00
e5106c9924
Hybrid selection performance statistics now include counts of the number of adjacent baits (0,1,2) using OverlapDetector and optionally include assayed bait quantities input via interval lists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2143 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 18:07:23 +00:00
87c1860398
I'm not sure I believe it, but JProfiler claims that calling FourBaseProbs.isVerbose() was taking 5% of my runtime...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2142 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 17:00:32 +00:00
b3f561710f
Optimizations:
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1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)
UG now runs in half the time for JOINT_ESTIMATE model.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 16:27:39 +00:00
rpoplin
depristo
ebanks
chartl
hanna
alecw
aaron
andrewk