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.
...
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
c0031b05ff
Stamp out lazy loading in the PluginManager. This is an attempt to stamp
...
out the non-deterministic VariantEvalIntegrationTest errors we've been seeing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4995 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 20:58:28 +00:00
02dc0f97d1
Remove testWalkerUnitTest; it doesn't actually do anything and just adds
...
extra cruft to the output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4993 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 19:02:00 +00:00
b107c97c1a
Cannot have "=" sign in reason, so change to ":"
...
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)
...
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
...
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
...
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
91824f478e
FASTQ directory is gone
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4986 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:16:06 +00:00
e3956148ac
removing unused fastqtobam
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4985 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:29:32 +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.
...
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
...
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.
...
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
5736d2e2bb
Something I should have done a long time ago: attempt to detect whitespace
...
after the line continuation backslash and enhance the error message if it
appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4981 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 23:15:08 +00:00
edebbb5aa0
Fixed long-standing bug reported by Mauricio where @Arguments assigned to
...
primitive types were properly validated and throw the proper
MissingArgumentValue UserException. Before this fix, the error reported
was the infamous DePristo BSOD (Could not create module String because
an exception of type NullPointerException occurred caused by exception null).
Thanks Mauricio!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4980 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 22:18:24 +00:00
6d855041ec
Oops...forgot to commit the changes that allow primitive VCF streaming.
...
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:
...
- 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
...
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
7916ab0ed5
remove the index each run
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4976 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:38:22 +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.
...
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
...
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)
...
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
...
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
...
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
8ba3a5a43f
Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.
...
GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 21:07:29 +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)
...
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
...
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)
...
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.
...
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.
...
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
...
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 "
...
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
...
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
3e7802a3e0
Minor changes to a qscript and the GQ constants on PrivatePermutations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4956 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 18:26:21 +00:00
79fcff13ff
Fixed import statement that was erroneously referring to VE3 rather than VE2.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4955 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 03:22:25 +00:00
f3ca2cc9de
Add safety net to BAQ calculation: explicitly cast to byte/int and check for bad values
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4954 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 18:09:12 +00:00
2ac5c52281
Better error message as per Mark
...
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
...
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
3163970ad5
Updates that slipped from my last commit: fixed some imports and calls to super().
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4951 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:34:40 +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.
...
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.
...
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
fdc514ded3
Intermediate commit for VariantEval 3.0. Among the changes:
...
* Stratifications (by comp rod, by eval rod, novelty, filter status, etc.) have been generalized. They are very symmetric with evaluators now. Each stratification can have multiple states (e.g. known, novel, all). New stratifications can be added and optionally applied. Some new stratifications include:
- by sample
- by functional class
- by CpG status
* Output is to a single file in GATKReport format, rather than having the options of CSV, R, table, etc.
* Rather than needing to state up front that the allowable variant type is a SNP or an indel, each eval record is inspected and the appropriate record type is fetched from the comp track. (This will require a bit more testing...)
* Evaluation context (basically a single row in a VariantEval report) generation and retrieval has been overhauled. Now, every possible configuration of stratification state is generated recursively and stored in a HashMap. The key of the HashMap is a key that represents that exact state configuration. When examining a comp track and eval track, this key is computed based on the data, providing easy lookup for the appropriate evaluation context. When there are only a handful of stratification configurations, this isn't a big deal. But when operating on a file with hundreds of samples, multipled by 3 states for novelty, 3 states for filtration, 3 states for CpG status, etc., it becomes a very big deal.
There are still some known issues:
* When the per-sample stratification is turned off, things are getting overcounted (too many variants are showing up when compared to the VariantEval 2.0 code). It's probably because I break out the VariantContext by sample even when not necessary, and those irrelevant contexts are still being counted. Or my recursion is overaggressively creating evaluation contexts, and they all get added up in a weird way. But that's why I'm committing now - so I can track down this issue without losing my work so far.
* The Jexl expressions are sometimes throwing an exception that I don't yet understand (they complain of an incorrect specification on the command-line... *after* the program has made it through a few thousand records.
* The request to have evaluations be smart enough to reject certain stratification states is not implemented yet.
There's still some work to do before I can replace VariantEval 2.0 with VariantEval 3.0, but feel free to take a look. I'd love comments on the new code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4946 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:20:24 +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.
...
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.
...
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
...
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
...
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.
...
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.
...
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
445ae06a7a
Re-add PrivatePermutations since ACTransitionTable is a little too memory-intensive to generate all the cuts that I need
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4937 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 06:11:18 +00:00
7cdaffbe5c
Create tmpdir if it doesn't exist.
...
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.
...
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.
...
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.
...
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
...
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
...
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.
...
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
...
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
...
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
...
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
...
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
...
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
...
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).
...
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
...
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
d70483c50a
Automatically filter out reads with consecutive indel operators in the CIGAR string
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4914 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 04:42:54 +00:00
848977678d
No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 22:06:19 +00:00
85f2968104
add convenience methods for RODs-for-reads: the ability to get all the RODs covering the read, regardless of their type or position on the read.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4912 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 20:46:03 +00:00
d7e74f8be6
Temporary phasing evalution walker that needs to be incorporated into the newest VariantEval, whenever it is available
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4911 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 20:43:15 +00:00
a31f6e4e99
Need to check isBiallelic before calling getSNPSubstitutionType for the allele swap warning
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4909 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 20:17:14 +00:00
8a0c07b865
Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4908 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 07:37:46 +00:00
6ebf5b30de
Transposing the table, and fixing some null pointer exceptions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4906 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 16:22:57 +00:00
cebfd01857
Properly output .bed
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4905 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 14:49:24 +00:00
464d0e18e3
Bringing us back to passing integrationtests
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4904 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 14:36:11 +00:00
8c583ea405
RBP now operates correctly at non-variant sites so we can phase hom-ref genotypes with -sampleToPhase
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4903 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-23 13:11:22 +00:00
376bc563d4
Trivial change to allow GenerateVariantClusters to be run on indels - not that VQSR now works on indels, far from it, but at least it's a first step and it allows us to generate cluster plots to see how well known/novel sites differentiate in their covariates (short answer: no difference/separation :( ).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4902 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 22:39:09 +00:00
e313eeede8
Push command-line expansions, such as BAM list unpacking and -B tag parsing, out
...
into the CommandLine* classes. This makes it easier for external functionality
(such as the VCF streamer) to use GenomeAnalysisEngine directly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4897 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 19:00:17 +00:00
66cca7de0f
renamed genotypesArePhased to isPhased, as the previous name was incorrect for several reasons. Added setPhase() to MutableGenotype. Other classes changed to reflect renaming to isPhased(). CombineVariants now supports an experimental MASTER mode where it consumes -B:master,vcf and -B:xi,vcf for any number i and updates the master with phasing information in xi.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4896 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 17:42:05 +00:00
2235245af0
PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 15:16:15 +00:00
a1653f0c83
Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable.
...
Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default.
Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call.
Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 02:38:06 +00:00
09c7ea879d
Merging GenomeAnalysisEngine and AbstractGenomeAnalysisEngine back together.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4889 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-21 02:09:46 +00:00
b3ac47812c
No longer emits records at filtered sites, in sub-sampling mode
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4883 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:43:50 +00:00
60880b925f
VC utils prune method now will keep genotype attributes as well as info keys. RBP now emits a far reduce (NO INFO, only GT:GQ:PG) records, further reducing size of phasing output
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4882 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:33:14 +00:00
8604335566
Minor improvements to further reduce debugging output. When running in -samplesToPhase mode, now only including the samples to phase in the output VCF, making it very much smaller.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4881 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:19:47 +00:00
ff90c24f28
RBP now supports operating on a subset of samples, outputting a much reduced VCF file appropriate for merging later. Also, general optimization to avoid printing enormous amounts of data to logger.debug by using a glocal static variable DEBUG that conditionally allows writing to the variable. Passes integration tests
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4880 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-20 16:03:28 +00:00
a3729bd59c
Now I call BeforeMethod correctly
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4872 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:45:45 +00:00
b7e4a015c0
static thread cache reset in UnitTest
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4870 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:53:10 +00:00
3bbc6a0540
Slightly more thread safe CachingIndexedFastaSequenceFile.java. Likely passes parallel testing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4869 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:05:17 +00:00
5dd0e8388b
Fixed a bug in UnitTest
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4867 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 19:44:35 +00:00
4a54f3f230
ThreadLocal version of CachingIndexedFastaSequenceFile. More efficient support for shared memory BAQ calculations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4865 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:44:48 +00:00
32d5397c01
Experimental support for sided annotations. Currently not more/less valuable than two-tailed testing. Future experiments are needed
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4864 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:08:31 +00:00
21dc05138a
Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4863 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 14:49:15 +00:00
2bd2667516
Another privately-owned class to add before re-checking out repository
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4858 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 18:14:51 +00:00
e406eb0f95
Adding a useful accessor method to TableFeature
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4856 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 18:11:51 +00:00
8ab4704b4c
Adding a command-line argument to allow missing values to evaluate as false instead of true
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4854 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 05:18:12 +00:00
9f3e56e487
VariantAnnotator shouldn't die when multiple records occur at the same position
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4853 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-16 04:05:47 +00:00
acfe83920b
'-L unmapped': adding integration tests for explicitly including (-L unmapped)
...
unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.
'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 23:11:46 +00:00
dabdeb729e
Eric broke the build. Eric broke the build.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4847 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 17:01:38 +00:00
5c0b66cb7c
3 big changes that all kill the integration tests: 1. Don't cap the PLs by 255 anymore. 2. Move over to the 3state model as the only available base model for UG (no more base transition tables). 3. New QD implementation when GLs/PLs are available.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4846 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 16:24:28 +00:00
5a27d231fa
Rename it so that nobody else falls into the trap laid out (the test is VariantToTable, the walker is Variant[s]ToTable)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4844 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:43:00 +00:00
5e27e9162f
Huh? I thought we parsed out comma-separated command line arguments into list automatically...just change the syntax of the integration test, no need to update the md5
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4843 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:40:27 +00:00
3e75431bc8
Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4842 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 03:33:36 +00:00
01323447c6
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
...
Fixed integration tests to wait on their own for the job to run instead of using SUB2_BSUB_BLOCK.
Updated VariantRecalibrationIntegrationTests MD5s which were knocked out of sync whele SUB2_BSUB_BLOCK was exiting in the middle of integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4840 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:57:20 +00:00
67c07d1a6a
Fixed recently introduced multiplexer issue where DoC couldn't be written
...
directly to command-line.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4839 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:35:15 +00:00
526ae92093
Getting back to '-L unmapped':
...
- basic unit tests for interval sorting and merging with mix of mapped/unmapped.
- validation to ensure that locus walkers (really all non-read walkers) blow up with a user error when -L unmapped is specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4837 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:24:18 +00:00
afd4655674
Use @Output instead of @Argument. As a side note, Chris I'm ready for this nightmare to go away...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4835 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 17:13:15 +00:00
cf7d932a17
Fix for f***ed up BWA alignments that adhere to SAM specs
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4834 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 17:12:25 +00:00
d550fdfd60
Disabling integration test to see if this restores the full test suite.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4833 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 15:27:02 +00:00
a5008faca8
Bug fix: when getting variant contexts at a site, we need to get only variants that start at current location, otherwise we get duplicated records when filtering indels.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4830 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 19:23:10 +00:00
17db2e0e24
(forgot I hadn't committed this) - refactored IndelStatistics module and added a new inner class to compute Indel classification along with other statistics. So, we now get an extra table specifying, per sample, counts of whether indels are:
...
- Repeat Expansions
- Novel sequence
And for indels of size <=2 we get a per-mononuc. or dinuc. breakdown of novels and expansions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4828 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 17:43:43 +00:00
cf75caf653
java changes:
...
VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-12 05:10:45 +00:00
abd6ce1c77
A TiTv-free approach for cutting variants! Apparently much better than previous approach, and will work for indels and SV will truly minor modifications to the code. Will discuss with methods group on Monday.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4822 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 23:08:13 +00:00
974aaa134d
Trival fix to broken build
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4820 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 13:56:03 +00:00
895cb39f41
Thanks to Platform Computing tech support, found the magical environment variable BSUB_QUIET.
...
Minor refactoring to add more of the CLibrary including setenv().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4819 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 21:27:12 +00:00
5b46a900b3
Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4818 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 19:35:12 +00:00
491a599b59
Minor optimization
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4817 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 18:56:35 +00:00
56433ebf6b
Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:
...
- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 04:36:06 +00:00
d4d3170436
Support for '-L unmapped' in read walkers. DO NOT USE THIS PATCH YET. It has been
...
subjected to and passes cursory testing on one dataset (and all integration tests pass).
However, there's a small library of validation checks, and unit and integration tests
that must be added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4813 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 19:51:48 +00:00
a2d6cef181
Weird corner condition fix in indel genotyper: if there are 2 consecutive locations on candidate sites to genotype, we can get both when calling getVariantContexts and if we are triggering on an extended event - this leads to confusion and we can end up picking the wrong one. So, we require start of the vc to be the same as the start of the ref locus to be sure.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4812 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 19:34:23 +00:00
722819688a
Minor utility improvements to ValidateBAQ
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4809 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-09 02:19:32 +00:00
a63bbb2fec
Optimized BAQ implementation. No longer does excessive amounts of copying of arrays. At this point I'm not 100% certain where additional performance improvements would come from
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4808 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 21:26:30 +00:00
db55b2b0c6
Better testing of BAQ. Now really handles soft clipped reads properly by doing an expensive copy operation :-( will need to be transformed to a ByteBuffer in the near future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4807 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 17:37:00 +00:00
f1f01610f8
Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4806 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 17:22:29 +00:00
16e1bbd380
Hidden command line option to control BAQ gap open penalty for testing by me and eric. ValidateBAQWalker has misc. useful improvements. PrintReads now adds BAQ tags on output, if requested.
...
BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 01:01:39 +00:00
1b6bec8e6b
Trivial changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4803 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 20:06:54 +00:00
ca7810f11d
First major update of indel genotyper:
...
a) Really fix this time strand bias computation for indels, previous version was a partial fix only.
b) Change way in which we deal with bad bases at the edge of reads. Even if a base is soft clipped in CIGAR string, there may still be dangling bases with Q=2 that may throw off QUAL computation in some sites. So, we're stricter and we also trim off those bases off read edges even if they are not soft-clipped officially.
c) First feeble-minded attempt at runtime optimization - don't compute log and 10^base_qual every time. Rather, cache 10^-k/10 and log(1-10^-k/10) for all k <=60. This speeds up code about 4x.
d) Further optimization: don't compute log(10^x+10^y) but rather use softMax function recently put into ExactAFCalculationModel.
e) Skip bad reads where all Q=2 (sic)
f) Avoid log to lin and back to log conversions of genotype likelihoods - this was legacy code from back when exact model did stuff in linear domain. This improves precision overall.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4802 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 18:35:22 +00:00
e2d45ec2af
Make Indel Realigner exceptions related to not enough space on disk or a too low file-handle limit UserExceptions.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4801 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 16:37:31 +00:00
70980b659a
CombineVariants no longer requires rod_priority_string
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4800 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-07 15:39:43 +00:00
bc885b7bd0
Don't print debugging output.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4799 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 20:57:11 +00:00
c91712bd59
BAQ calculation refactoring in the GATK. Single -baq argument can be NONE, CALCULATE_AS_NECESSARY, and RECALCULATE. Walkers can control bia the @BAQMode annotation how the BAQ calculation is applied. Can either be as a tag, by overwriting the qualities scores, or by only returning the baq-capped qualities scores. Additionally, walkers can be set up to have the BAQ applied to the incoming reads (ON_INPUT, the default), to output reads (ON_OUTPUT), or HANDLED_BY_WALKER, which means that calling into the BAQ system is the responsibility of the individual walker.
...
SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 20:55:52 +00:00
5d2c2bd280
Just refactoring into utils/baq directory
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-06 17:43:43 +00:00
80f32712dc
Tiny bug fix
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4793 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:48:33 +00:00
44feb4a362
Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4792 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:29:39 +00:00
8901e63879
Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4791 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 04:36:21 +00:00
bef48e7a42
For Chris, to make his life easier: iterate over all VCF records passed in looking for one with an ALT allele defined instead of assuming all records have one.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4789 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 02:23:38 +00:00
97c94176c0
Immediate, obvious bug fix to avoid blowing up on unmapped reads
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4788 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:43:39 +00:00
a5b3aac864
Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4787 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:23:06 +00:00
b12cec4302
Added emitOnlyMNPs flag
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4785 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 20:34:17 +00:00
6d4ec7f9e7
Remove RefSeq INFO from MNPs since annotating them properly
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4784 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 19:03:35 +00:00
4719bbc772
Changed dontRequireSomeSampleHasDoubleAltAllele parameter to mean that merging should only start at a polymorphic site
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4783 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 17:52:56 +00:00
ec174dc0ba
As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4782 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:37:08 +00:00
92cf7744a6
Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4781 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:31:13 +00:00
237ab1d489
1. As discussed in group meeting today, because we cap BQ by MQ, if MQ < minBQ then we filter the read.
...
2. Update to UGCalcLikelihoods for Chris: require a vcf bound to 'allele' to be provided so that we know exactly which alternate allele we should be calculating GLs for at each site. The user is warned when the VC is not biallelic or there are multiple records at a site.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4780 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 05:57:06 +00:00
da6a07ad3b
First round of critical fixes to indel genotyper (more to come tomorrow):
...
a) Avoid complete crash of caller that broke due to a recent refactoring by someone who must not be named <cough>EB<cough>... an integration test to avoid this in the future coming soon.
b) Fixed up strand bias computation for indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 02:48:09 +00:00
e09d6ee56b
write non-MNP VariantContexts records only once (where they start)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4777 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:14:26 +00:00
1515bf6de9
Merged common VCF writing logic into phasing/WriteVCF.java
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4776 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:03:02 +00:00
4e62de4213
Added method getOriginalReadGroupId(): takes merged (in case of collision) read group id as reported by a read coming from the merged stream and returns this read's read group id as it was listed in the original input bam file.
...
IndelRealigner now uses this functionality to correctly un-mangle read group id's in --nWayOut mode (i.e. when we need to write reads into separate output bams with headers matching the original inputs).
Some hidden changes to IndelRealigner: purely testing and development, transparent to the users (hidden option added)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4775 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 21:41:52 +00:00
e5282742f9
Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4774 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 18:43:24 +00:00
0adf505b53
We no longer look at by-hapmap validation status in the VQSR because using the HapMap VCF file is higher quality. As a side effect we now support the dbsnp 132 vcf file. ApplyVariantCuts now requires that the input VCF rod bindings begin with input, matching the other VQSR walkers. Wiki updated with information about how to obtain the hapmap and 1kg truth sets.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4772 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 15:38:45 +00:00
99b942b0b4
Removing duplicated header args
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4770 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 20:16:53 +00:00
9ac0f98d0d
Fixed bug in retaining proper RefSeq records
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4768 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 18:39:02 +00:00
7caf666f48
For Sendu: add a hidden option to allow bams to come out unsorted. We've agreed to let him deal with sorting these puppies on his own.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4767 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:56:13 +00:00
3afa841a6a
Fixing docs
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4766 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:36:47 +00:00
6a6cdc1925
Adding minor usage docs
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4765 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:34:33 +00:00
0d1c905df3
Adding UGCalcLikelihoods and UGCallVariants so that GSA members can break up the calling process into separate steps (calculate the GLs and then call off of those) - useful for Chris's new batch merger. As the docs say, these are absolutely not supported or recommended for public use.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4764 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:32:26 +00:00
b4ef716aaf
As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4763 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 16:42:08 +00:00
0892daddb0
Improvement for the TGEN folks: when running in the solid recal mode of SET_Q_ZERO_BASE_N, update the NM tag if one was present in the read to reflect the new N's in the read.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4761 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 04:36:44 +00:00
a22b1b04e6
SW-turbo. Kind of. This implementation is presumably equivalent to the old one (mathematically), but runs ~10 times faster: inner loops eliminated completely. The author of the original implementation should be sentenced to the galleys. Oh, that would be me...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4760 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 00:08:47 +00:00
2ac938fe4e
1)
...
Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:08:25 +00:00
af84462f3e
The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4757 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 17:19:54 +00:00
21256909bb
Not supported. I'm checking this in for Ryan only.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4756 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 16:59:18 +00:00
e21a66d876
Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.
...
Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 15:29:40 +00:00
7f2ded0706
belated special case fix for Menachem; if the results of a BTI and BTIMR produce an empty interval list, exception out. This would be solved long term with better handling or empty and / or null interval lists. I'll add a JIRA
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4754 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 05:49:20 +00:00
a181680814
We no longer require dbSNP files to be of the dbsnp rod-type; VCFs will do (provided they are bound to the name 'dbsnp')
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4753 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 03:25:18 +00:00
8ffea42b75
about 10% improvement in SW alignment (and hence IndelRealigner!) speed by using c-style linearized array representation for matrices instead of java 2D arrays...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4751 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:06:50 +00:00
b03ac61e9d
consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4750 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:01:56 +00:00
abc13d0a90
Temporary hack: force abort with an intelligent message suggesting that users
...
specify -B:dbsnp,vcf <filename> if the filename passed if the --DBSNP argument
value contains 'vcf'. We'll replace this functionality once dbSNP 132 starts
playing nicely with the tagging system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 23:37:30 +00:00
d89e17ec8c
Fare thee well, UGv1. Here come the days UGv2.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4747 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:51:19 +00:00
727dac7b7a
Added MNP annotation of the number of AA changes occuring in the SAME RefSeq entry (numAAchanges), and if this number is > 1 for any of the alt alleles (alleleHasMultAAchanges)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4746 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:24:30 +00:00
222cd42ceb
Have the UG engine take care of the GL to PL conversion. Note that we still use GLs for calling (since we are losing precision in high-pass and, even worse, it can affect QD), but we emit PLs in all cases. This means that calculating the GLs, emitting them to VCF, and then calling off of them (a la samtools) is absolutely, positively not ideal.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4745 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 20:28:16 +00:00
102c8b1f59
Large refactoring of the UGv2 engine so that it is now truly separated into 2 distict phases: GL calculation and AF calculation, where each can be done independently. This is not yet enabled in UGv2 itself though because I need to work out one last issue or two. Tested on 1Mb of 1000G Aug allPops low-pass and results are identical as before. Also, making BQ capping by MQ mandatory.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4744 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 21:36:33 +00:00
ce051e4e9a
Write to sdout when no -o is provided
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4743 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 06:19:26 +00:00
e3e6d176df
Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4736 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 18:40:34 +00:00
35b90d2295
Don't compute SB for ref calls
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4735 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 03:54:26 +00:00
6934f83cc7
Two changes to CombineVariants.
...
1. Fix: VCs were padded before the merge, but they were never unpadded afterwards. This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-25 04:52:12 +00:00
d775192631
Check if MNP annotation of amino acid is dependent on the MNP, or could it be obtained through some single-base variant?
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4733 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 22:38:33 +00:00
0dd40c3684
Updating doc text
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4732 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:34:14 +00:00
ed08899abc
Overwhelming evidence that maxQ = 50 is now a better default than maxQ = 40 in the base quality score recalibrator, especially when combined with dbsnp build 132. Also, added option in ProduceBeagleInputWalker for Beagle-ing chromosome X calls with male samples which sets the genotype likelihood for the AB allele to zero for those samples.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4731 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:32:26 +00:00
ca70ed611c
Totally revamped the MNP annotation and put it in its own walker: AnnotateMNPsWalker
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4730 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 18:05:10 +00:00
8768e1a240
Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 14:59:16 +00:00
7a8b85dd15
Catch the JEXL exception when trying to match a variable that's not in the context - and don't filter in these cases. Now everyone can happily go back to using the stupid (and hopefully temporary) AlleleBalance filter.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4727 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 05:00:41 +00:00
caf2c21f61
Must close the writer to flush the cache
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4726 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:33:08 +00:00
816c33c821
indel-related fixes to the strict validator
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4725 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:08:34 +00:00
9cdc341be5
Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4724 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 01:45:44 +00:00
ea6e2218c1
1. dbsnp has some massive indels which my left-aligner was barfing on because there isn't enough reference context; fixed. 2. Lower default calling threshold to Q30 for UGv2.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4722 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 19:28:33 +00:00
53672361cc
capture more details when something IO-related goes wrong in writing a Tribble index
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4720 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 17:06:28 +00:00
082073ca3c
Stop RBP.getPileupBySample() from throwing a NullPointerException if the
...
sample doesn't exist -- now returns null.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4719 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 05:17:06 +00:00
787e5d85e9
Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.
...
Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 22:59:42 +00:00
8ca5edf89f
Fix issue where non-required file inputs can throw a NullPointerException
...
rather than a UserException when an the input argument is specified without
an argument value.
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4714 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 01:49:17 +00:00
b9a59ea54f
Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-21 04:24:42 +00:00
cff7c6ddce
These are user exceptions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4712 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-21 02:08:11 +00:00
374c0deba2
Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4711 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 19:59:05 +00:00
c723db1f4b
Added a -summary jexl argument to VariantEval similar to -validate.
...
Updated the package of ValidationGenotyper to match the file location.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4710 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 04:42:46 +00:00
79725f2d9c
Excluding the QFunction log files from the set of files to delete on completion.
...
When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 20:22:01 +00:00
721e8cb679
VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:54:59 +00:00
8cba86a69d
Trivial code organization for the haplotype score
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 12:32:55 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
90711d445c
Change the interface for RMDTrackBuilder, therefore always mandating the specification
...
of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 19:00:17 +00:00
367cc9135f
Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 18:19:56 +00:00
2f3578182a
Added VERY preliminary version for merging refseq annotations as SNPs are merged
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4698 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:49:12 +00:00
e2f7f33ce7
Added getIntegerAttribute()
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:33:07 +00:00
d86ab2becb
JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:08:16 +00:00
delangel
hanna
fromer
depristo
rpoplin
carneiro
aaron
kshakir
ebanks
chartl
kiran
handsake
asivache
bthomas