bfbf75fe3e
Fix error in command-line validation: don't ever allow intervaled access to unindexed read stream, no
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matter what type of traversal it is.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4997 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 02:49:04 +00:00
00310c05bb
Fix corner condition that happens when there are indels right at the end of a contig and there's not enough reference to build a haplotype.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4996 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 21:08:22 +00:00
b107c97c1a
Cannot have "=" sign in reason, so change to ":"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4991 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:23:44 +00:00
b4a2112a0d
Added the "previous locus" to interesting sites VCF (locus with respect to which the site is phased)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4990 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:19:20 +00:00
e8f0ae4b09
Renamed and documented some phasing-specific classes to make their purpose clearer to someone browing through the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4989 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 16:17:36 +00:00
ffae7bf537
Moved phasing-specific utilities to phasing sub-directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4987 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:38:20 +00:00
ce3d226183
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4984 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:12:30 +00:00
e0092bb160
Experimental feature: change the rate at which log messages appear on-the-fly
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and enable/disable performance logs from outside the JVM process. Making this
available for the moment; we'll see whether it ends up being useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4983 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 04:20:53 +00:00
9e93091e9a
-baqGOP now takes phred scaled scores instead of probabilities in the command line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 00:06:38 +00:00
6d855041ec
Oops...forgot to commit the changes that allow primitive VCF streaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4979 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 21:54:51 +00:00
8a6b126ea8
Several cleanups to IndelMetricsByAC:
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- No longer a standard eval module to keep integration tests happy
- Remove class name overlaps with SimpleMetricsByAC so that modules don't overwrite each other's files, and to make it easier to grep results.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4978 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:35:24 +00:00
8fe5641b2e
can explicitly set the now required ReferenceDataSource in unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4977 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:25:12 +00:00
468ef382b7
vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4975 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:32:27 +00:00
bdd382198c
Necessary changes to enable HaplotypeScore annotation for indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4974 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:09:12 +00:00
23597a2bde
Variant Eval module that collects indel statistics (basic counts and event sizes) and partitions by AC (similar to SimpleMetricsByAC in the SNP case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4973 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:08:09 +00:00
48052907a6
A hom genotype can always be considered phased
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4972 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-11 18:48:48 +00:00
c2dd956888
Moved PrintReferenceVariantsWalker to playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4971 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 22:07:41 +00:00
ee348ac9d4
Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 20:27:04 +00:00
01c2091cd9
A LocusWalker to print the haploid reference genome as a VCF file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 16:59:41 +00:00
9648399630
Boneheaded silly bug in indel caller - posterior probability computation was using priors gotten from SNP heterozygosity, not indel heterozygosity. Added then indel het. argument to command line and hook it up (not a radical change in calls though, just a few dubious calls around the edges fall off)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4967 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 14:56:28 +00:00
b24e1134f9
unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:32:50 +00:00
b34e2f733f
Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.
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Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:03:36 +00:00
60f45a7c49
Stupid me. Forgot to put this check in the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4959 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:16:41 +00:00
56b87da8f9
a better error message for the situation where a RMD track generates a negitive length interval; the user will now see a message like "Bad input: A feature produced by the reference metadata track named "bed" at position chr1:10434-10433 has a start greater than the stop; this is an invalid position "
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4958 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:06:04 +00:00
4272b824d6
unused imports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4957 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 18:33:12 +00:00
2ac5c52281
Better error message as per Mark
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4953 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:44:02 +00:00
e0d091b3db
Die gracefully if the bam is malformed with quals that are too high
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4952 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:39:08 +00:00
d88fd7212f
Changes to allow the primary key of a table to be hidden. Formatting changes to account for when that column is hidden.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4948 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:27:19 +00:00
307c41c128
Changes to allow the primary key of a table to be hidden. Formatting changes to account for when that column is hidden.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4947 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:26:38 +00:00
e9201b81d1
A more general method for specifying samples to act on from the command-line. Supports samples specified individually on the console, a file of samples, or regular expressions to select multiple samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4945 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 14:54:56 +00:00
5e9a8f9cb3
Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.
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Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 22:25:08 +00:00
cba436fa2f
small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 21:20:26 +00:00
4b37710bcd
Added validator for phasing using read information, e.g., PacBio: ReadBasedPhasingValidationWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4940 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 20:05:56 +00:00
d203f5e39a
Experimental change in how we classify indels - up to now, an indel of say AA was counted as a 2-mer repeat expansion. But in reality, if the event is sounded by A's it's really a multiple monomer expansion. So, we first reduce the indel bases in case they are made of repeated elements before classifying them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4939 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 17:13:18 +00:00
4ac0590744
Fix for NaNs in the rank sum tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4938 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 15:21:30 +00:00
7cdaffbe5c
Create tmpdir if it doesn't exist.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4936 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 03:07:11 +00:00
0982d35f5b
Bug fixes in streaming in Tribble data via /dev/stdin.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4935 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 02:43:04 +00:00
23dbc5ccf3
HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4934 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 00:28:05 +00:00
85714621be
Better interface to Genotypelikelihoods class. Now you need to specify the format (GL vs PL) of the output string when calling getAsString(). All likelihoods are represented as GLs internally. QualByDepth no longer does its own conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4933 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-04 21:48:14 +00:00
96729acd0d
Optional argument to put the original position into the INFO field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4930 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-04 19:22:44 +00:00
caedfed860
Fix bug where indels being incorrectly classified in VariantEval module
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4929 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-04 18:01:48 +00:00
8d2c14b29c
Update Picard / sam-jdk at Tim's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 02:17:25 +00:00
d31c658c2e
Organized performance monitoring passes unit tests and is more efficient
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4924 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 02:09:08 +00:00
c51e745bae
The engine can be null in a unit test, so check for it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4923 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 01:00:52 +00:00
75a7d8a76e
Trivial formatting error
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4922 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:44:36 +00:00
5539c2d9f3
--performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4921 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:34:21 +00:00
4c9746f463
Disabled performance log intermediate commit. Will be refactored and committed to the responsiblity along with documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4919 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 22:18:12 +00:00
3fc9862964
Unit test fixed - Tribble codecs aren't designed to be stateless, but I was
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using one as though it was. Fixed, and debug code reverted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4917 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 17:47:52 +00:00
b9cb57f4b9
A unit test is failing on bamboo in a way I can't reproduce (or even explain).
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Checking in some debugging info.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4916 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 16:35:04 +00:00
cba18116e4
A significant refactoring of the ROD system, done largely to simplify the process of
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streaming/piping VCFs into the GATK. Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build
RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
are the walkers that feel the need to access the ROD system directly. (We need to stamp out
this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs. These'll be
fixed as part of the VCF streaming project.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 04:52:22 +00:00
hanna
delangel
fromer
rpoplin
carneiro
depristo
ebanks
aaron
kshakir
kiran