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
0e089ce0b7
watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4966 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-09 13:09:30 +00:00
298dce2940
Adding the native jna support libraries from the jna.jar to the Queue package jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4965 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-08 10:48:30 +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
be67161b47
Deleting old shell code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4962 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:36:16 +00:00
e64a300642
Deleting old python code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4961 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:33:45 +00:00
3362f0c280
Private mutation simulator and analysis routines for EOMI paper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4960 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 21:23:29 +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
3e7802a3e0
Minor changes to a qscript and the GQ constants on PrivatePermutations
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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.
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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
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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
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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
3163970ad5
Updates that slipped from my last commit: fixed some imports and calls to super().
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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
3b76034d50
Namespace changes to avoid conflicts with other packages.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4950 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:33:26 +00:00
ab143c82af
Selects only the project requested via the Oracle command, rather than selecting everything and then subsetting.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4949 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-06 15:32:32 +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
fdc514ded3
Intermediate commit for VariantEval 3.0. Among the changes:
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* 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.
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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
48772a9d01
Fixed bug that required users to use the recordOriginalLocation option
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4944 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 23:12:14 +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
20f29e4690
In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4941 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 20:30:55 +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
445ae06a7a
Re-add PrivatePermutations since ACTransitionTable is a little too memory-intensive to generate all the cuts that I need
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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.
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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
d9270b2363
Fixed recordOriginalLocation option to work properly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4932 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-04 19:58:13 +00:00
8de33924e8
Added recordOriginalLocation option perl script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4931 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-04 19:52:50 +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
5583fa179b
Now uses PNGs and a very high downsampling value to more clearly display the information
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4928 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:57:51 +00:00
dba30c4118
Subsampling of points, for the case where we have enormous numbers of points
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4927 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:48:11 +00:00
54adbd2581
Added instantaneous rate plotting routine to performance log plotter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4926 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 13:33:35 +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
586d3f05d9
Better cumhist function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4920 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-02 23:32:20 +00:00
ebanks
fromer
delangel
depristo
kshakir
aaron
chartl
kiran
carneiro
rpoplin
hanna