aaron
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99ddd8ab15
|
bug fix for transitioning between chromosomes in GLF output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1237 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-14 17:58:04 +00:00 |
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aaron
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01fc8da270
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adding the GenotypeLikelihoodsWalker, which generates GLF genotype likelihoods that are pretty much identical to the samtools calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1235 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-14 16:57:18 +00:00 |
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aaron
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36819ed908
|
Initial changes to the SSG to output GLF by default
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1231 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-14 08:46:04 +00:00 |
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aaron
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e4152af387
|
added a big speed-up for interval list input processing. With large interval sets this was taking way too long...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1227 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-13 22:00:00 +00:00 |
hanna
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9f0fb9f3aa
|
Fix for GSA-90: GATK banner and error messages should point to the wiki website.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1226 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-13 21:56:41 +00:00 |
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hanna
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b18caa2052
|
Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1225 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-13 20:42:12 +00:00 |
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hanna
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5c321f9630
|
Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1223 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-13 16:41:55 +00:00 |
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hanna
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b61f9af4d7
|
Cleaning up, preparing to incorporate a better fix for Eric's problems with validation stringency in BAM files opened directly from the walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1222 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-13 01:42:13 +00:00 |
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hanna
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aa4f60d980
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Make sure that only reads marked as 'mapped' are filtered based on validity of alignment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1217 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-10 17:44:06 +00:00 |
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hanna
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03e1713988
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Better support for specifying read filters to apply directly from the walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-09 23:59:53 +00:00 |
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aaron
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d86717db93
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Refactoring of the traversal engine base class, I removed a lot of old code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-09 21:57:00 +00:00 |
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hanna
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60a86fb34a
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Better handling of fasta files with non-standard extensions.x
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1206 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-09 18:18:48 +00:00 |
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aaron
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8ee5c7de8e
|
GLF reader and writer check in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1202 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 23:06:37 +00:00 |
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hanna
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da4d26b1ea
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Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 20:26:16 +00:00 |
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aaron
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e106cf73d8
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A quick change to provide more verbose output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1197 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 19:08:19 +00:00 |
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hanna
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433ad1f060
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Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 18:49:08 +00:00 |
ebanks
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787c84d68b
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only compare pair position for paired end reads
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1190 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 04:07:08 +00:00 |
andrewk
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d3daecfc4d
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Added unit tests for function in ListUtils to randomly sample lists with replacement, updated AlleleFrequencyEstimate to provide a callType of HomRef, HetSNP, HomSNP, update indices in CoverageEval.py, and made a lot of changes to CoverageWalker biggest one being that it directly calls SingleSampleGenotyper instead of implementing some parts of SSG itself.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1189 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-08 02:05:40 +00:00 |
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hanna
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4ba2194b5e
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Filter reads whose alignment starts past the end of the contig to which it allegedly aligns.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1188 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 22:27:44 +00:00 |
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hanna
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5d7393d7cb
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Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1183 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 15:18:05 +00:00 |
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aaron
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033bafe7a1
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fixed sam by reads test for the new filtering code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 05:45:50 +00:00 |
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aaron
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2a86f2f833
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an initial pass at the GLF reader, and some other genotype changes to phase out the LikelihoodObject I created.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1179 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 04:30:27 +00:00 |
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hanna
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5735c87581
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Basic infrastructure for filtering malformed reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1178 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-06 22:50:22 +00:00 |
depristo
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b9d533042e
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Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-06 22:02:04 +00:00 |
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hanna
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d19366eaad
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Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-06 15:41:30 +00:00 |
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andrewk
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dcb8892568
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Lot of code for coverage evaluation tools including first version of python script to evaluate the downsampled SSG callls made and the java code to make all the calls at Hapmap chip sites at various downsampling levels; ListUtils contains functions for randomnly subsetting lists (with replacement) which are useful for subsetting the same elements in both the reads and the offsets lists of a LocusWalker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1162 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-03 08:07:02 +00:00 |
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depristo
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6684cb8bc9
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copySamFileHeader() utility function
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1154 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-02 12:55:51 +00:00 |
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aaron
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d4d3af20f2
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made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-01 21:35:34 +00:00 |
asivache
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7462f3f344
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Bug in setContig() fixed: sequence dictionary's .getSequences().contains() and .getSequences().indexOf() do NOT work when applied to contig names (Strings), since getSequences() returns a list of SAMSequenceRecord's; changed to querying the dictionary directly for specified contig name
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1147 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-01 20:50:09 +00:00 |
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hanna
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b43d4d909e
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Fix CleanedReadInjectorTest to work with new CleanedReadInjector.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1142 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-01 15:48:06 +00:00 |
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aaron
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f5cba5a6bb
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Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-30 19:17:24 +00:00 |
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asivache
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177d6d00b8
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added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1130 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-30 17:40:37 +00:00 |
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aaron
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d7d4298917
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Some files to support generic genotype outputing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-26 15:43:41 +00:00 |
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depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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aaron
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0c3aabd1c5
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logger output should be less verbose by default. Also fixed a printout in my read validation walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1102 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 19:47:29 +00:00 |
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aaron
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4e04370f14
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forgot a file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1096 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 17:56:17 +00:00 |
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ebanks
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ea2426dcd0
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one more change needed to commit
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1093 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 15:09:53 +00:00 |
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aaron
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61ce4e5983
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quick doc change
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1086 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-24 16:35:46 +00:00 |
kiran
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3112302ec9
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A priority-queue-like container that allows you to add a specified number of elements. When the limit has been reached, new additions replace the lower scoring elements.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1083 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-24 15:39:47 +00:00 |
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depristo
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0a50f2e160
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Updated and near final version of tabular recalibration system. Uses 'yates' correction for low-occupancy quality bins. Faster and more robust handling of input and output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-24 03:52:12 +00:00 |
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hanna
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ef546868bf
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Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-23 23:48:06 +00:00 |
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aaron
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4a92a999a0
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made the constructors protected. Protected also mean package-protected, so other methods in the utils class can call these constructors (mainly the parser), as well as any inheriting classes. Also fixed some Intellij suggested clean-ups and documentation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1071 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-22 16:01:59 +00:00 |
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aaron
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bcb64d92e9
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Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-22 14:39:41 +00:00 |
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depristo
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8ac40e8e2d
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Updated version of the recalibration tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-19 17:45:47 +00:00 |
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ebanks
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aef519b427
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more comparisons
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1059 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-19 16:46:05 +00:00 |
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kiran
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0a0ef573f7
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Methods for finding classes given a path and finding classes that implement a given interface. This stuff was mostly copied from private methods in WalkerManager, so there's some code redundancy. At some point, those calls could be replaced with these.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-18 22:43:19 +00:00 |
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depristo
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d748c85dc4
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Cleaned code and reorganized -- moving in the right direction for v2
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-18 22:28:34 +00:00 |
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aaron
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b947fd586f
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FIxed a nasty bug in GenomeLoc compareContigs; we were using '==' to compare Integer contig ID's. The surprising thing is that it actually works for Integers > -127 and < 128 (they're cached by the JVM, so it's actually comparing the underlying ints). Switched over GenomeLoc contigs to int based.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1033 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-17 20:19:47 +00:00 |
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hanna
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43a28750e0
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Package level documentation -- helps new users get acclimated to the codebase more quickly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-17 16:27:48 +00:00 |
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depristo
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7d281296a7
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Finishing checking for building
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-17 14:12:40 +00:00 |