298cc24524
Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1296 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 22:37:41 +00:00
cac04a407a
For Manny: filter out reads where the the ref index ==
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NO_ALIGNMENT_REFERENCE_INDEX but the alignment start != NO_ALIGNMENT_START.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1295 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 21:19:24 +00:00
9c12c02768
AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 17:54:44 +00:00
6e4fd8db4a
Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1290 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 22:23:28 +00:00
b43925c01e
Switched to Reflections ( http://code.google.com/p/reflections/ ) project for
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:32:22 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 00:55:52 +00:00
129ad97ce5
performance improvement to GenomeLocParser -- moved regex pattern compile out of local field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1272 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 02:56:25 +00:00
107f42a01e
Hacks for getting GLFs support in the Rod system working
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1268 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 21:03:47 +00:00
692b1e206f
stop throwing an exception here: we don't always have allele counts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1259 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 20:34:01 +00:00
5be5e1d45f
added conversion from iupac format and new rod to deal with FLT file format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 18:34:41 +00:00
9ecb3e0015
adding GLFRods with tests and some other code changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 15:30:19 +00:00
99ddd8ab15
bug fix for transitioning between chromosomes in GLF output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1237 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 17:58:04 +00:00
01fc8da270
adding the GenotypeLikelihoodsWalker, which generates GLF genotype likelihoods that are pretty much identical to the samtools calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1235 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 16:57:18 +00:00
36819ed908
Initial changes to the SSG to output GLF by default
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1231 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 08:46:04 +00:00
e4152af387
added a big speed-up for interval list input processing. With large interval sets this was taking way too long...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1227 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 22:00:00 +00:00
9f0fb9f3aa
Fix for GSA-90: GATK banner and error messages should point to the wiki website.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1226 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 21:56:41 +00:00
b18caa2052
Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1225 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 20:42:12 +00:00
5c321f9630
Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1223 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 16:41:55 +00:00
b61f9af4d7
Cleaning up, preparing to incorporate a better fix for Eric's problems with validation stringency in BAM files opened directly from the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1222 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 01:42:13 +00:00
aa4f60d980
Make sure that only reads marked as 'mapped' are filtered based on validity of alignment.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1217 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 17:44:06 +00:00
03e1713988
Better support for specifying read filters to apply directly from the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 23:59:53 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
60a86fb34a
Better handling of fasta files with non-standard extensions.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1206 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 18:18:48 +00:00
8ee5c7de8e
GLF reader and writer check in.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1202 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 23:06:37 +00:00
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
e106cf73d8
A quick change to provide more verbose output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1197 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 19:08:19 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
787c84d68b
only compare pair position for paired end reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1190 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 04:07:08 +00:00
d3daecfc4d
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1189 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 02:05:40 +00:00
4ba2194b5e
Filter reads whose alignment starts past the end of the contig to which it allegedly aligns.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1188 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 22:27:44 +00:00
5d7393d7cb
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1183 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:18:05 +00:00
033bafe7a1
fixed sam by reads test for the new filtering code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:45:50 +00:00
2a86f2f833
an initial pass at the GLF reader, and some other genotype changes to phase out the LikelihoodObject I created.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1179 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 04:30:27 +00:00
5735c87581
Basic infrastructure for filtering malformed reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1178 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:50:22 +00:00
b9d533042e
Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:02:04 +00:00
d19366eaad
Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 15:41:30 +00:00
dcb8892568
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1162 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 08:07:02 +00:00
6684cb8bc9
copySamFileHeader() utility function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1154 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 12:55:51 +00:00
d4d3af20f2
made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 21:35:34 +00:00
7462f3f344
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1147 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:50:09 +00:00
b43d4d909e
Fix CleanedReadInjectorTest to work with new CleanedReadInjector.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1142 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 15:48:06 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
177d6d00b8
added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1130 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 17:40:37 +00:00
d7d4298917
Some files to support generic genotype outputing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:43:41 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
0c3aabd1c5
logger output should be less verbose by default. Also fixed a printout in my read validation walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1102 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:47:29 +00:00
4e04370f14
forgot a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1096 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:56:17 +00:00
ea2426dcd0
one more change needed to commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1093 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 15:09:53 +00:00
61ce4e5983
quick doc change
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1086 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 16:35:46 +00:00
3112302ec9
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1083 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 15:39:47 +00:00
hanna
depristo
aaron
kcibul
ebanks
andrewk
asivache
kiran