c78a72e775
Applies Fisher's Exact Test to determine whether there's a strand bias and, if so, filters the call out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1193 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:14:11 +00:00
b211f500a3
Applies secondary base feature to variants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1192 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:13:29 +00:00
6e31057e6b
Some changes involving output of marginal calls to different, per-filter files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1191 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:12:57 +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
194b75613b
Fix compile problem with unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1187 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 20:29:31 +00:00
1db15ee468
made some things protected so that I can inherit them in MultiSampleCallerAccuracyTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1185 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:50:28 +00:00
1fa71aa31d
Now outputs stats. Doesn't do the downsampling thing because I think I'll have enough counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1184 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:29:31 +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
f6a273a537
other fixes for some broken unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:53:13 +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
31313481f6
Temporary patch to filter out bad alignments that aren't quite fully reported as bad.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1176 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 18:41:55 +00:00
6580211c2a
First version of depth of coverage filter. Right now it takes in a maximum coverage threshold given by the user.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1175 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 18:22:46 +00:00
fac7ac5142
Don't print out 0 coverage (which is always 0)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1174 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 17:44:32 +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
000d92a545
added gc calculation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1172 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 13:07:04 +00:00
338cdbebad
deal with screwy solid reads in the cleaner (no cigar strings)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1171 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:49:58 +00:00
8bcbf7f18a
First draft of multi sample caller accuracy test.
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Doesn't do it's job yet but the pieces are in place.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1170 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:29:13 +00:00
4019cd2bd7
Added ROD for parsing hapmap3 genotype files.
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Tweak to TabularROD to allow HapMapGenotypeROD to work.
Added HapMapGenotypeROD to list of RODs in ReferenceOrderedData.java.
Modified MultiSampleCaller to return a single object with most of the relvant information.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1169 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:28:24 +00:00
e5e249d4ac
temporary fix to deal with screwy SOLiD reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1168 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 03:25:57 +00:00
cf1854b339
Fix for monsterous problems with solid data -- now can dynamically expand recalibration tables on the fly as reads declare additional read groups -- use assumeFaultyHeader flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1167 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 17:15:49 +00:00
bcda66d2db
Simple performance improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1166 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 16:45:23 +00:00
0d00823332
Fix for performance bug in extending the read with X's in cases where the read is aligned off the end of the contig.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1165 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 16:17:38 +00:00
be2f8478c0
added supression of failure messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1164 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 15:19:37 +00:00
25c30b12bb
added MAF-style output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1163 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 15:10:19 +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
d603145cb0
Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1160 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 20:38:10 +00:00
62807139fc
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:54:01 +00:00
6a25f0b9c5
refactored into new package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1158 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:37:54 +00:00
1c83b4d949
forgot to take out some test code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:18:37 +00:00
bc17ff567a
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:15:50 +00:00
47cb9f169e
Stable tool that's the reverse of merging -- splits a file into individual BAM files, one for each sample ID in the SAM header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1155 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 12:56:46 +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
bb92eb8b1c
added a fix for overlapping reads in the locus context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1153 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 02:08:59 +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
c2e5a68aaf
output format changed in --verbose --somatic mode: now also prints the <#reads with indels>/<coverage> for normal samples, rather than only for the tumor; also, code cleaned up a little
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1149 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:56:16 +00:00
4cbf069de1
First version of coverage evaluation tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1148 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:52:25 +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
76fd4b3848
deal with different contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1146 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 19:17:27 +00:00
20fab507a8
Choose the REF if it scores equal to consensus!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1145 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:54:27 +00:00
9b182e3063
Prep for documenting command-line arguments: delete some arguments that don't make sense any more given
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the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:23:35 +00:00
5a5103cfd2
Heads up, everyone: command-line args no longer need to be public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1143 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 16:09:22 +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
d58eeb7539
Don't cry wolf: only one warning is now emitted, instead of tons of warnings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1139 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:50:37 +00:00
a3e0ec20c4
Kill the TraverseByLocusWindows traversal. TraverseLocusWindows will take its place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1138 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:46:35 +00:00
93da64db10
Update naming for consistency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1136 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 22:03:21 +00:00
e93f751bd7
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 21:59:54 +00:00
8d3dc57c3d
Commit to emit in sorted order so we don't have to use /tmp
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1133 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:47:15 +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
9fca79ed62
Read groups are now sorted in the output data, for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:50:44 +00:00
08df4771c8
count X/N/etc. as mismatches for the NM attribute in the BAMs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1127 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:55 +00:00
d412c5dc2f
Updated to use SecondaryBaseAnnotator class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1126 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:43 +00:00
e3cdf7ef4b
A single class that can be handed reads for training and basecalling. When in training mode, we accumulate no more than 10000 reads and always replace the lowest-quality reads with superior quality reads. Thus, the training set always contains 10000 of the best reads available. After training is complete, the class can be interrogated to return the SQ tag for a given RawRead object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1125 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:03:15 +00:00
8aa3b65e7f
fix to guarantee emission in sorted order
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1122 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 13:48:41 +00:00
03f8177a53
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:51:55 +00:00
1dcababad1
a fix to make the test run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:24:32 +00:00
a17bf145f6
fix to respond to the change in IndelLikelihood constructor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1119 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 19:05:33 +00:00
7ecc43e9a7
Fixed subtle null ptr exception discovered by Kiran. Now deals with the rare situation where you have only say Q28 bases at dbSNP sites, so you fail in the Table recalibration step with a null pointer error into the data structure indexed by quality score. If you are Q score above those seen before you aren't modified in any way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1118 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 18:57:42 +00:00
95e2ae0171
Deal with reads whose ends are aligned off the end of a chromosome.
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Includes update to ignore non-ATCG bases (not just 'N')
(Also, create a BWA dir for future work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1117 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:50:05 +00:00
65a788f18a
Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.
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Some doodling around with indel calling in an EM context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:32:12 +00:00
ceeeec13b8
Computes a vector of numbers of reads falling into successive intervals of specified length (e.g. numbers of reads per every 1Mbase)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1115 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:12:21 +00:00
eb74b16e39
updated what constitutes removing entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1113 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 18:29:00 +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
1a97c86f95
don't crash when an unmapped read is encountered, just write it into the output file, it should be ok
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1111 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:33:59 +00:00
491ed70b44
TraverseByLocusWindow -- asstd bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:51:38 +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
73caf5db15
This is, strictly speaking, NOT a GATK module. Standalone, picard-level executable except that it uses couple of gatk utils (GenomeLoc). Remaps alignments from cutom reference (such as transcritome, hyb-sel etc) onto the 'master' reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1107 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:04:18 +00:00
ee2af3b423
I committed this too soon... reverting...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1106 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:49:12 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
23680a9a16
Replaced an expensive sort with an inexpensive direct computation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1104 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:25:12 +00:00
83816fb801
Stop using the annoying refIterator (temp change until new traversal is green lighted)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1103 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:05:39 +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
11d83ac7d0
pushing up to test on unix box
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1101 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:00:48 +00:00
0d9041380d
remove printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:54:14 +00:00
0a16519aa2
a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:32 +00:00
2c97c5e873
Compute a simple histogram of depth of coverage.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1098 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:11 +00:00
102b38c055
Sketch of new version of TraverseByLocusWindow, and a flag to conditionally turn it on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1097 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:20:56 +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
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
3b24264c2b
incorporating skew check, further output of metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1094 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 16:01:07 +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
347608cfe0
remove hacked traversal in preparation for move to Matt's new one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:32:05 +00:00
940d75171a
Big cleaner changes:
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1. Added a Walker to merge intervals before cleaning
2. (Almost) all Walkers can filter out 454 reads (and do by default)
3. Got rid of -all command and related pieces (time to switch to CleanedReadsInjector)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1090 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:31:24 +00:00
3cb6d7048e
don't freak out if two reference intervals a custom contig is built of are strictly adjacent; instead politely warn user that her data suck and proceed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1089 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 19:08:10 +00:00
d4f3ca1a10
A utility class for keeping the mapping from 'custom' reference (e.g. transcriptome) onto the 'master' reference (e.g. whole genome), and for remapping SAM records from the former onto the latter. It's Arachne's BaitMultiMap, pretty much
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1088 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 18:16:15 +00:00
69dc502174
I forgot that this depends on BoundedScoringSet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1087 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 17:18:53 +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
a9c30c5fcc
added -nosort cmdline flag; if specified, the output writer does not attempt to sort reads on the fly (sorting involves use of sorting collection backed up by temporary disk storage and can lead to crashes if temp size is low and/or filesystem is not behaving). Output can be later sorted externally by samtools
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1085 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 15:58:00 +00:00
7b5d8d7604
Changed the intensities array order from cycle,channel to channel,cycle. This, I'm told, is a far more efficient allocation strategy.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1084 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 15:41:06 +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
0a50f2e160
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 03:52:12 +00:00
ef546868bf
Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
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Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 23:48:06 +00:00
dfa2efbcf5
not crashing when refseq annotation track is not requested is a nice added feature
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1079 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 22:52:40 +00:00
eb999f880a
incorporating skew check
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1078 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 19:51:51 +00:00
1339f3f3e3
make refseq annotation file an optional argument; if specified, indels will be annotated as genomic/utr/intron/coding (accidentally appearing 'unknowns' probably mean that there's something wrong with refseq annotations?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1077 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 18:17:03 +00:00
9c0dba6979
Some quick documentation and typo changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1076 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 13:40:13 +00:00
cb9c6f18ef
spelling fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1074 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 01:46:35 +00:00
630d9e6a37
Fixed a typo.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1073 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:37:46 +00:00
8b4d0412ca
Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:11:18 +00:00
4a92a999a0
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
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1071 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 16:01:59 +00:00
9e25229014
use better entropy threshold and don't print out "new" SNPs (since they're just an antrifact of the low (arbitrary) threshold
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1070 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 15:30:08 +00:00
bcb64d92e9
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
26eb362f52
Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 21:27:40 +00:00
d3f0c51944
longer update times so we don't overwhelm when running genome-wide
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1067 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 14:10:02 +00:00
a21c2a7e48
don't make mapping quality too high
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1066 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 04:51:42 +00:00
686c8133ed
massive change in the way the cleaner works, mostly revolving around the fact
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that we no longer trust indels from the alignments (although we do use it as
a good alternate consensus possibility).
Other changes include better "greedy mode" performance and allowing the user
to have just the cleaned reads themselves be printed out (mostly for Matt's
CleanedReadInjector).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1065 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 03:56:59 +00:00
9e26550b0d
Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 16:00:23 +00:00
dde52e33eb
Cleanup of the cleaned read injector based on Eric's feedback.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 22:04:47 +00:00
a0a3cf2f9f
VariantFiltrationWalker can now apply specified exclusion tests after the feature tests. For a given variant, all reasons for exclusions are printed to screen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1061 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 21:12:01 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
aef519b427
more comparisons
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1059 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 16:46:05 +00:00
58b132ee10
Eliminate redundant computation.
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Still room for more optimization, but I called chr20 (60Mb) in a couple hours on the queue this morning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1058 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 16:31:57 +00:00
3a1b58ca65
remove unused argument lodThreshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1057 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 12:40:12 +00:00
9a0151b7e1
Added an option to list all available feature classes and exit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1056 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 00:00:12 +00:00
ed7afd8b70
Added javadocs. Now throws an exception if an unknown feature is specified. General cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1055 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 23:28:38 +00:00
284fd6a5fb
VariantFiltrationWalker now inspects its parent package and determines the list of features that can be applied. Command-line specification of filters to run look at the simple names of these features and do a case-insensitive match to determine which features to apply. A new verbose mode allows the user to see how the likelihoods are changing with the application of each subsequent feature.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1054 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:45:36 +00:00
0a0ef573f7
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1053 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:43:19 +00:00
d748c85dc4
Cleaned code and reorganized -- moving in the right direction for v2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:28:34 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
1bca144119
Moving things around
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:06:46 +00:00
ca8a3bd85e
Another temp checking for rearranging things
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1048 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:04:36 +00:00
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
03fe166994
Wrote a public static version of loadFirstNReasonableReadsTrainingSet() so Alec can call it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1046 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 20:18:17 +00:00
a4fa02f11c
Moved output outside of for loop so I don't have 10 different versions of the same variant (though, now that I think of it, that's not necessarily a terrible thing for debugging...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1045 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:59:26 +00:00
768a16e791
An experimental, tile-parallel version of the secondary base annotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1044 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 19:58:09 +00:00
e26df45e8e
Different features can now be specified by repeatedly supplying the -F "featurename:arguments" option.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1043 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 18:45:03 +00:00
7a921c908c
Can now adjust the genotype likelihoods of a variant returned from the rod. This automatically causes the lodBtr, lodBtnb, and genotype to be recomputed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1041 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:26:37 +00:00
9a7cec7d2e
Directory to house variant calling and filtration tools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1040 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:20:38 +00:00
5992d88409
skip N's in the reference (rather than crash. doh!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1039 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 23:22:35 +00:00
c4d9058f32
Added module rodVariants.class to the list of allowable RODs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1037 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:33:13 +00:00
ab2a80f3ea
A new ROD type that allows one to input a geli.calls file back into a walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1036 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:32:21 +00:00
9ef391706c
Added outputting of genotype posteriors to geli.calls file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1035 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 21:31:46 +00:00
615572ea06
output to out... not System.out...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1034 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 20:43:10 +00:00
b947fd586f
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1033 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 20:19:47 +00:00
cba9025983
More package-level documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1030 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:28:45 +00:00
43a28750e0
Package level documentation -- helps new users get acclimated to the codebase more quickly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:27:48 +00:00
673205ed5f
additional output tweaking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1028 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 15:37:38 +00:00
7d281296a7
Finishing checking for building
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 14:12:40 +00:00
d1e25bfe88
Intermediate checkin for safety -- now compiles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1026 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:16:55 +00:00
2250769a42
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1025 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:07:19 +00:00
86c8c08375
Intermediate checkin for safety -- do not use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1024 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 13:06:24 +00:00
78b7fb25c7
allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:23:12 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
4f6d26849f
Behold MultiSampleCaller!
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Complete re-write of PoolCaller algorithm, now basically beta quality code.
Improvements over PoolCaller include:
- more correct strand test
- fractional counts from genotypes (which means no individual lod threshold needed)
- signifigantly cleaner code; first beta-quality code I've written since BaitDesigner so long ago.
- faster, less likely to crash!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1020 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 20:03:24 +00:00
7db4497013
fixing the readTraversal output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1019 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 19:44:38 +00:00
b11c5a7cd5
doing some read validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1018 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 19:25:43 +00:00
010304fe44
bug: printing incorrect coordinates into output, finally fixed (?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1017 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 18:08:56 +00:00
647b8a1ab0
Fix TabularROD printing and testing so Aaron stops nagging me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 15:49:26 +00:00
a0a549557f
added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file.
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Also fixed a bunch of documentation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1015 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 22:15:03 +00:00
2259dc3a8f
added filtering out indels with large levels of noise (mismatches) remaining in the close proximity; also a bug in recording deletion coordinates is fixed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1014 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 21:13:28 +00:00
a6477df6d1
Now optionally outputs whether "SNPs" are maintained/cleaned out/introduced by cleaning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1013 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 20:02:02 +00:00
11aa715630
added capability for filtering by platform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:19:50 +00:00
8f4bc8cb6e
Move filtering functionality into the PrintReadsWalker. More to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 16:38:08 +00:00
161c74716c
Forgot to change some direct references to variables in SSG. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1009 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 14:16:18 +00:00
9eeb5f79d4
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1008 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:21:08 +00:00
f2946fa3e8
Various refactoring to achieve hapmap and dbsnp awareness, the ability to set pop-gen and secondary base priors from the command-line, and general code cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1007 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 07:20:22 +00:00
f6af190b74
ignore clipped reads for realigning indel positions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1006 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 01:01:27 +00:00
0583459839
Another formatting change to make Hapmap sites more clearly visible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:53:21 +00:00
811f560efb
add refseq annotations to single sample calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1003 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:43:30 +00:00
e9be2a9c60
Changed a formatting issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:40:32 +00:00
ca09a10b76
refseq annotation rod is now manually bound to tell coding indels from non-coding ones
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1001 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 19:27:37 +00:00
5859948e80
Fixed bugs in CleanedReadInjector arising from integration testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@999 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 17:37:33 +00:00
fb7ba47fff
Now does really neightbor distance calculation, as well as true snp cluster counting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@998 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 16:29:26 +00:00
dbf2cc037c
don't have a null-pointer hissy fit when the reference is N.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@997 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 13:59:16 +00:00
4eda040e0f
what used to be internal cutoff values are now exposed as cmdline parameters: minCoverage, minNormalCoverage, minFraction, minConsensusFraction
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@995 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:22:52 +00:00
41687d5237
Added accessors for the prior probabilities.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@994 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:16:10 +00:00
12dd18cdba
Now aware of Hapmap and dbSNP sites. We *can* change the priors there, but we don't yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@993 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:15:34 +00:00
d5cd883b99
bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@992 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 21:03:15 +00:00
a12009e9e7
Added a new constructor in which priors for hom-ref, het, and hom-var can be specified. Otherwise, it uses the default values of 0.999, 1e-3, and 1e-5 respectively.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@991 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:33:45 +00:00
909fefa40a
Argumentized priors for hom-ref, het, and hom-var.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@990 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:32:44 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
032d0436e6
Added ROD for 1KG SNP calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 19:53:51 +00:00
ffffe3b2f6
-Support for 1KG SNP calls in RODs
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-Minor bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@987 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:56:37 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
599ceeddd8
Better method for downsampling deep regions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@983 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:57:40 +00:00
4d9a88153a
Update inferred insert size of cleaned reads when they are paired
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@982 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 16:29:13 +00:00
3796654069
Added walker to emit intervals of clustered SNP calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@981 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 00:57:14 +00:00
678ddd914f
Stopgap fixes GFF, DbSNP being half-open rather than half-closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 21:38:57 +00:00
94b0e46d12
checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:46:16 +00:00
8d25f1a105
should be a little faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@978 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:33:45 +00:00
026f68fb41
a couple of quick name changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:02:52 +00:00
72a81f8f25
removed the requirement that a bam file list be present in the XML version of the command line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@975 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:01:13 +00:00
b1f90635c1
1. downsample when there are too many mismatching reads (needs perfecting)
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2. allow user to specify that no reads be emitted
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@974 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:55:42 +00:00
39dcd4f11f
an attempt to bail out when unmapped reads are reached at the end of the file(s). still testing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@973 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 19:53:50 +00:00
030efc468f
added naive ad-hoc cutoff for the pile size the cleaner will attempt to process; use --maxPileSize argument to force any pile larger than specified cutoff to be directly written to the output without cleaning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@972 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:52:35 +00:00
f9be175f44
Be smart about trying alternate consenses:
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try prior indels first and only 1 instance of them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@971 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:43:22 +00:00
f304803811
initial check-in of an easy way to create command line tools based on the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@970 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:34:02 +00:00
b0cc763eb5
Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:31:00 +00:00
9ebcd6546d
Convenience printing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@968 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 17:07:38 +00:00
06e5a765f8
now has two modes: one sample - just call indel sites; two samples - call somatic-looking variants only. Still uses heuristic count-based cutoffs, cutoffs are hardcoded and are pretty conservative...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@967 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:41:38 +00:00
5451bbfd5a
-move final vars to command-line args
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-Per Andrey: ignore indels from aligner when testing against alt consensus
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@966 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 16:39:00 +00:00
ad80894afa
Bumped picard to latest svn version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:36:34 +00:00
ec2f015447
fixed a bunch of comments and license headers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:10:46 +00:00
6bb7f7e9d8
Commented some stuff out so that things compile.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@963 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 14:06:33 +00:00
dc6a9ca196
Pooling resources to lower memory consumption.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 13:39:32 +00:00
87ba8b3451
Removed some useless code. Don't apply second-base test if the coverage is too high, since the binomial probs explode and return NaN or Infinite values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@961 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:27:06 +00:00
a12ed404ce
Changed method name from applyFourBaseDistributionPrior to applySecondBaseDistributionPrior. 'Cause that's how I roll.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@960 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:21:22 +00:00
3adb4239e4
Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:19:31 +00:00
2b0e7f612b
Handles bam pileups where some of the reads have SQ tags and some don't.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@958 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:17:15 +00:00
36c98b9d6c
added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 01:52:25 +00:00
eb962fe52a
adding an artificial sam file writer, used to unit test some of the walkers (mainly the PrintReadsWalker)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@956 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 21:47:49 +00:00
e77dfe9983
Allow script to be easily modified to support different platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@955 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 16:06:57 +00:00
7fa84ea157
10x speedup of recalibration walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 15:39:40 +00:00
a62bc6b05d
fixed some documentation and attached a correct license
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@953 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:44:27 +00:00
bf6190b471
cleaned up the PrintReadsWalker, and added a lot of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@952 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:28:32 +00:00
b45b1d5f2b
border case bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@951 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 04:33:15 +00:00
fecba2cae5
Disabled option to show secondary quals as the definition has changed to conform to the spec and thus this printout is non-sensical.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@950 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 03:21:14 +00:00
e7f222108d
More accessors. Can compute the sum of the quality scores in the read (useful for sorting) and can return a subset of itself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@948 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:02:48 +00:00
6506504a60
Updates after seeing a certain number of reads, not a certain number of bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@947 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:01:36 +00:00
65d0675a4e
Some changes regarding what to do when a cycle is completely busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@946 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:01:13 +00:00
0bd78d72d7
Some changes regarding what to do when a cycle is completely busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@945 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:00:33 +00:00
af0b03a257
Added tests for mostFrequentBaseFraction() and reverseComplementString()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@944 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:53:45 +00:00
681e67c72c
Added some methods to generate random bases or random base indexes, optionally disallowing the generation of a specified base or base index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@943 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:47:54 +00:00
13eb868536
helper class. array-like random access and fast shift. good for sliding windows (e.g. keeping coverage over last 100 bases while sliding along the reference)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@942 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:11:57 +00:00
3d6e738a60
still under development. does not genotype yet, but walks and talks (counts overal coverage and indel variant occurences at every reference position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@941 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:10:31 +00:00
58f7ae8628
better filtering, plus deal with case where user doesn't input maxlength
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@939 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 18:44:29 +00:00
ce431b5d2d
added hashCode()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@937 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 16:52:02 +00:00
b4ef16ced2
extractIndels() now should deal correctly with soft- and hard-clipped bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@936 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 16:04:49 +00:00
a8a2d0eab9
added support for the -M option in traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@935 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 15:12:24 +00:00
e2ed56dc96
Add a MAX_READ_GROUPS sanity parameter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@934 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 13:57:43 +00:00
9f35a5aa32
Insidious bug: clipped sequences (S cigar elements) where a) processed incorrectly; b) sometimes caused IntervalCleaner to crash, if such sequence occured at the boundary of the interval. The following inconsistency occurs: LocusWindow traversal instantiates interval reference stretch up to rightmost read.getAlignmentEnd(), but this does not include clipped bases; then IntervalCleaner takes all read bases (as a string) and does not check if some of them were clipped. Inside the interval this would cause counting mismatches on clipped bases, at the boundary of the interval the clipped bases would stick outside the passed reference stretch and index-out-of-bound exception would be thrown. THIS IS A PARTIAL, TEMPORARY FIX of the problem: mismatchQualitySum() is fixed, in that it does not count mismatches on clipped bases anymore; however, we do not attempt yet to realign only meaningful, unclipped part of the read; instead all reads that have clipped bases are assigned to the original reference and we do not attempt to realign them at all (we'd need to be careful to preserve the cigar if we wanted to do this)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@933 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 05:20:29 +00:00
3a8219a469
use knowledge from other reads to find a consensus
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@932 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 21:22:17 +00:00
596773e6c6
Cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@931 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 20:25:08 +00:00
98396732ba
Bug fixes for Andrey
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@930 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 18:19:51 +00:00
b48508a226
indelRealignment() signature changed. The only difference about consensus sequences is that they are passed along with alignment cigars that start inside the sequence, while for 'conventional' reads cigar always starts at position 0 on the read. Logically, indelRealignment() should not know what 'consensus' is. Instead, now it receives an additional int parameter, start of the cigar on the 'read' sequence
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@929 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 17:42:19 +00:00
9eb38c0222
mostly synchronizing with the main branch. Based on anecdotal evidence (too few examples in the data), realignment (shifting indel left across a repeat) works correctly on non-homonucleotide repeats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@928 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 16:39:16 +00:00
c6634e3121
cleaned up some code and minor bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@927 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 03:14:21 +00:00
99c105790b
Now indelRealignment should be correct... The old version could only condense to the left homo-nucleotide indels. New version should be able to detect and shift left arbitrary repeated sequence (e.g. deletion of ATA after ATAATAATA will be shifted left to the first occurence of ATA on the ref! NOT THOROUGHLY TESTED YET, will test tonight../somaticIndels.pl --dir . --cutoff 100 -filter EXON --mode SOMATIC --condense 5 --format bed > 0883.indel.somatic.exon.100.bed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@926 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 23:54:07 +00:00
3b4dc6e7b5
added sequencePeriod(String seq, int minPeriod) - finds smallest period equal to or greater than minPeriod for the specified text string seq; this is a trivial (hopefully correct) back-of-the-envelope implementation for a well-known and well-studied problem; there should be more efficient algorithms in the wild
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@925 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 23:05:24 +00:00
40ac3b7816
Inject read group into covars_out file's toString output. Continue fixing systematic bug in the code where flattenData is not joined to the read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@924 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 20:43:28 +00:00
0bb4565798
added AlignmentUtils.getNumAlignmentBlocks(read) - a faster alternative to read.getAlignmentBlocks().size(); IntervalCleaner updated accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@923 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 19:35:21 +00:00
92b054b71b
moved another variant of numMismatches to AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@922 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 18:07:48 +00:00
7018dd1469
moved another variant of numMismatches to AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@921 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 18:05:29 +00:00
ac5b7dd453
Fixed order-of-operations bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@919 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 03:22:56 +00:00
819862e04e
major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 23:34:37 +00:00
400399f1b8
fixed (?) a bug in insertion realignment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@917 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 22:04:37 +00:00
34bb43a6c8
Saw that one of the offsets needed to be changed from - 1 to -2 and changed the wrong damn offset. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@915 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 19:18:34 +00:00
4623a34ad3
Fix bug in realigning insertion cigar strings
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@914 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 18:46:41 +00:00
199be46c36
changed the warning that is outputted when the GenomeLoc constructor can't find the given contig in the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@913 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:49:03 +00:00
092a754071
Make sure indel position from SW alignment is leftmost possible
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(and improve printouts)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@912 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:36:10 +00:00
37efd78c7e
fixed the logger call so we get output that indicates this class generated the message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@911 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:02:17 +00:00
b323c58ef2
add a place to store the walker return value, along with a method to retrieve it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@910 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 14:41:42 +00:00
36fb6ca3c5
Allow user to specify the compression to be used when writing out BAM files.
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Updated most of the walkers to reflect this change.
Now it won't take forever to write BAMs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@909 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 08:48:34 +00:00
c1792de44f
First pass at fixing the incorrect border-case behavior of the cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@908 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 07:55:06 +00:00
9da04fd9ac
Cleaned up error warning in case no PL groups are present.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@907 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 03:14:17 +00:00
45eeefbb80
Deal with randomly occurring unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@906 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 02:55:53 +00:00
fdfc3abf80
Better handling for case where PL attribute is missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@905 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 02:52:30 +00:00
9689bb3331
Very early draft of script integrating the covariant counting / logistic regression. Deleted some unused code and spurious debug info.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@902 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:52:11 +00:00
109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
4d880477d6
Deal with ends of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@900 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 20:09:53 +00:00
40bc4ae39a
The building blocks for segmenting covariate counting data by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@899 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 19:55:24 +00:00
13be846c2a
qualsAsInt argument for Pileup -- fixing stupid bug [again]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:52:12 +00:00
97c8ff75dd
qualsAsInt argument for Pileup -- fixing stupid bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:51:17 +00:00
9de3e58aa8
qualsAsInt argument for Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:37:39 +00:00
4d654f30d4
slightly improved error message printed upon failure to parse interval list file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@895 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:24:43 +00:00
bcc7bacba1
added List<Transcript> getTranscripts(); also more comments added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@894 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 16:25:14 +00:00
b492192838
Pairwise SNP distance metrics now enabled
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@892 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 00:11:29 +00:00
8672ae6019
Now seeing results from the training data. There are still some critical problems in the quality of the output, but we're at least getting training output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@891 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 20:41:07 +00:00
4e41646c88
print out stats for Andrey
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@890 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 17:45:35 +00:00
dfe464cd81
Updated CovariateCounterWalker to be read group aware
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@889 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 10:06:06 +00:00
40af4f085c
Adding some utilities to test unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@887 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 07:40:34 +00:00
fa93661133
Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@884 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 22:41:10 +00:00
107b5d73b5
The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@883 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 21:23:56 +00:00
a1218ef508
changed default value for failure output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@880 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 19:32:29 +00:00
7e7c83ddca
fixing insidious bugs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:33:45 +00:00
6e60cddfed
A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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e. Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way. Right now, hasNext() isn't guaranteed to be correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:14:46 +00:00
ad5b057140
parameterized a bit more
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@877 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 17:58:26 +00:00
587d07da00
Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@876 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 16:55:05 +00:00
82aa0533b8
added some more documentation to the GLF writer and it's supporting classes, and some other fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@875 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 14:53:58 +00:00
c4cb867d74
basic clustering of reads to reduce artifacts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@873 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 02:54:21 +00:00
e712d69382
GLF writing support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@872 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 21:30:18 +00:00
417f5b145e
Strand test and misc touch-ups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@871 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 17:13:21 +00:00
fc91e3e30e
equals signs can be important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@870 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:56:21 +00:00
4edb33788b
added a fix for a bug Andrew found
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@869 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:53:56 +00:00
b7defeae83
Fix bug in unit tests created by new filter in TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@868 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:50:44 +00:00
fc7320133c
Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@867 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:34:38 +00:00
f19d7abba9
Added geli compatibility mode to SingleSampleGenotyper, to enable easy linking to the geli2popsnps.py script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@866 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 14:32:12 +00:00
4d6398cef9
a lot of people have been asking me for the equivalent of the old "PrintCoverage" command from Arachne. Even though I show them the pileup, and they agree that's more accurate/complete, they don't want to modify their scripts and/or write a translator. It was simple enough to write, so here it is.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@863 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-31 01:45:23 +00:00
c04b67c969
Basic instrumentation support for the hierarchical microscheduler.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@862 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:19:27 +00:00
c8347c3c94
set proper package name (...walkers.indels), remove couple of unused import statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@861 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:02:14 +00:00
c549c34caa
still in development and testing; kinda works
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@860 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:59:03 +00:00
c252fec1bc
synchronizing, no real changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@859 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:56:14 +00:00
eafdba7300
more efficient implementation of line parsing, runs at least 1.5 times faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@858 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:09:06 +00:00
8761ab3aff
Oops. IteratorPool was occasionally creating too many RODIterators in cases where some reference-ordered data was missing. Fixed by better tracking position of RODIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@857 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:00:31 +00:00
d601548d53
added reallocate(int[] orig_array, int new_size) and int[] indexOfAll(String s, int ch); the former is self-explanatory, while the latter returns array of indices of all occurences of ch in the specified string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@856 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 20:15:00 +00:00
a1edb898ef
Make criteria for determining whether to stop and merge inputs more sane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@855 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 18:08:18 +00:00
fe3b843b65
intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@854 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 15:56:55 +00:00
e0803eabd9
enabled underlying filtering of zero mapping quality reads, vastly improves system performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@853 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 14:51:08 +00:00
1f93545c70
Always opt to merge dictionaries when creating a SAMFileHeaderMerger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@852 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 22:38:16 +00:00
0cf90b6f8a
Tie into sequence merging code in the latest version of picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@851 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 21:48:35 +00:00
b43deda6c9
iterative changes to GLF files; also a test of checking-in over sshfs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@850 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:24:30 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
19f9ac2b05
Realign existing indels (from the aligner) to leftmost position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@848 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 04:56:51 +00:00
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 01:35:49 +00:00
d275c18e58
adding some objects we need for the GLF format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@846 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:32:25 +00:00
ce6a0f522b
First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:02:24 +00:00
a11bf0f43e
Basic unit tests for ReferenceOrderedView, ShardDataProvider. Addressing GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@844 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 21:15:01 +00:00
e533c64b8f
Walker to pull out the reference for given intervals and emit them in fasta format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@843 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:39:09 +00:00
5c6163ecbf
Removing the old reads traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@842 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:36:11 +00:00
c7b032cc88
missed a file in the add.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@841 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:27:38 +00:00
3c3cd5bb64
Moving some of the data sharding around. A new shard catagory now exits, INTERVAL. This saved a lot of code that was mirroring the same approach in both the read and locus shard strategies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@840 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:24:31 +00:00
99524ab6d0
package name corrected
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@839 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:20:43 +00:00
b76f8c4eb5
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@838 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:33 +00:00
c3678c7bb9
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@837 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:08 +00:00
5b310e48f5
changed to use factored out Transcript class; some docs added (not much)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@836 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:17:23 +00:00
ae0bac5696
'made public' implies the 'public' keyword, actually...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@835 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:57:01 +00:00
41c1a62ac4
formerly private class, factored out and made public. Represents a transcript annotation (transcript id, genomic location, genomic intervals for all exons present in this transcript, etc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@834 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:52:38 +00:00
8edba13ded
Unit tests for the reference views. Partially addresses GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@833 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:49:45 +00:00
9bd6489f8e
Output indels in the format appropriate for low-coverage indel submission
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@832 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:32:15 +00:00
919e995b7f
-Moved my walkers to indels directory
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-Removed entropy walker and replaced it with mismatch (column) walker
-Some improvements to the cleaner (more to come)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@830 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 16:34:24 +00:00
864a1e81e3
Delete stale class from previous rethink of the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@828 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 13:52:03 +00:00
6fab1a64fa
Started work on GLF input / output basics. Do not use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@827 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:49:59 +00:00
b81135c606
bug fixed; this rod seems to work now...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@826 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:25:34 +00:00
a488d2dbb2
Lazy creation of output streams. Only create output streams when absolutely necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@824 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:56:57 +00:00
ab7bb5800a
forgot to remove debug print statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@823 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:38:27 +00:00
568a0d3c27
exon coordinates are now parsed correctly (?). IF DELIMITER IS THE LAST CHARACTER IN A STRING, String.split() DOES NOT return empty field as the last one; instead, the last field returned will be the one immediately before such delimiter! Wicked.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@822 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:36:50 +00:00
f4119c17de
still working on it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@821 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:07:38 +00:00
d73f2e95cc
refseq added to the list of known rod types
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@820 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:06:44 +00:00
23b7a28015
simple walker that works off pre-computed tumor/normal genotyping calls (e.g. samtools pileup). Collects overal stats and also writes somatic variants into IGV-compatible bed file if asked to. NOT finished. NOT tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@819 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:05:47 +00:00
8f1cabd33d
cmd line args changed - again; internally uses VariantType enum
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:58 +00:00
9ef1a21112
minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@817 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:06 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
4edcdffe45
refseq annotation track: should be able to provide (multiple) transcript annotations available over a given genomic position. NOT finished and NOT tested!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@815 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:07:15 +00:00
149cc9989b
spaces!!!!!!!!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 19:40:25 +00:00
c2df35b7fe
- get leftmost position of indel correct
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- don't try to clean reads with mapping quality of 0
- un-deprecate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 17:24:58 +00:00
54bb643d19
Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 15:58:21 +00:00
008d677bea
Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy.
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Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-23 20:50:28 +00:00
d056f9f3e8
Changed the name to reflect the sorted nature of the set, added some fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 22:34:24 +00:00
831d430025
Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:52:40 +00:00
34413362fd
Bugfix: handle case where queue is empty.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@808 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:45:22 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
cd80e3f372
Replaced dumb training function with a version that creates a training set slightly more sensibly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@806 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:34:33 +00:00
02c0afdb85
Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:33:34 +00:00
454a6d1df7
Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:32:20 +00:00
2a5be1debe
Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:12:00 +00:00
02fc4f145f
refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 18:54:40 +00:00
4b718688d5
no changes, really, just synchronizing (instead of reversing) to increase the amount of entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@801 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:27:28 +00:00
893f1b6427
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:50 +00:00
a9dfbfb309
internal changes and some refactoring. slightly different final report. Now can take tracks that implement either Genotype or GenotypeList; takes an arg specifying what variants to look for (POINT - aka snp - or INDEL); takes an arg specifying whether default ref/ref call of one type (INDEL/POINT) should be implicitly assumed if another call (POINT/INDEL respectively) was made at the same position [this is probably most useful for indels and only (?) for sam pileups: if we have only point mutation call at a given position, it does mean that we do have coverage, and that there was no evidence whatsoever for an indel, so we have an implicit 'no-indel' call]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@799 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:09 +00:00
d5bb4d9ba9
Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@798 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:20:01 +00:00
732fed9aad
ALERT, ALERT! rodSAMPileup is now a GenotypeList, not a Genotype! Now it can intelligently read full samtools pileup files (containing, in general, both point and indel genotypes at the same position). No need to split/synchronize pileups from different individuals anymore, hooray!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@797 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:17:59 +00:00
26633957d9
Genotype interface is extended: now it requires implementing object to be able to tell whether it isPointGenotype() or isIndelGenotype() (and the contract requires, e.g. alleles to be represented differently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@796 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:14:46 +00:00
d9fc84f1e3
actually checking in the first pass
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:13:27 +00:00
8773b3a430
a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@794 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:12:01 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
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compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
9902ce8073
properly flush the gzip output stream. this was a subtle inheritance bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:57:58 +00:00
63caca31bf
minor update in report printout format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:56:09 +00:00
7afc10fd6f
updated, reports more stuff now, including stats for external consistency checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@789 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:28:18 +00:00
30c63daf89
More improvements to the duplicate quality combiner, making progress towards a clean system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:26:57 +00:00
65995887fc
Releasable version of the Pileup walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@786 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:37 +00:00
dc17a5661d
Better accessors for dealing with second base prob pileups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:16 +00:00
d261459c48
Useful function to create a string with N copies of a same char
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@784 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:23:52 +00:00
287bb52e81
Refreshes the mount points that we'll be using (so that the program will play nicely with LSF).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:36:12 +00:00
b5ad5176f7
stick headers on the output tables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:50 +00:00
83e1454a11
Added a method to determine the fraction of a sequence that's taken up by the most frequent base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@781 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:31 +00:00
bdf772f017
Added test for determining the fraction of a sequence that's taken up by the most frequent base (quick-and-dirty homopolymer testing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@780 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:08 +00:00
d61a5261c1
Better integration of reference-ordered data into the data sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@779 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:09:32 +00:00
0d58e4ccc9
-check original alignments for indels when computing mismatch score
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-move logging to debug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@778 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:55:42 +00:00
5f67914b08
Added loads of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@777 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:40:47 +00:00
1a9d5cea29
Added a method to reverse-complement a String object, preserving 'N' and '.' bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:39:39 +00:00
a687c6bc03
Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@774 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:54 +00:00
324ef9cbd1
Test class for PathUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@773 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:22 +00:00
8515247575
Adding some functions I keep reinventing, especially for testing purposes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@772 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:30:44 +00:00
e6200fe5b5
don't ignore reads when maxReadLength isn't set
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also, print out LOD score for cleaning
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:24:10 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
7e77c62b49
auxiliary class, a simple struct to keep together info like numbers of covered, assessed, ref/variant bases across the sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@769 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 16:30:16 +00:00
7e5e422591
ReferenceOrdereData now inspects the ROD class using reflection. If the ROD declares a static Iterator<ROD> createIterator(String rodName, File rodFile) factory method, it is wrapped and used by the ReferenceOrderedData to read records from rodFile. If the ROD does not provide such factory method, the old behavior is the default: ReferenceOrderedData uses its own simple default iterator to read the file line by line (assuming there is only one line per record/position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@768 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 15:23:22 +00:00
26dd3cd50e
Cleanup. Move filtering functions closer to where they're used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@767 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 21:42:48 +00:00
e7a6f8cdc4
Removed evidence of a previous incarnation of data sharding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@766 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 20:48:33 +00:00
3cad580655
Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@765 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:17:16 +00:00
dc748d9c9c
Integrate more feedback on command-line argument system. Focus on help
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formatter: separate required from optional but otherwise keep ordering
the same, reorder GATK arguments by usage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@764 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:01:25 +00:00
34f9820299
update mapping quality score and edit distance attribute for reads when they are cleaned
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@763 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:51:31 +00:00
57918de753
add the @Requires for this walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@762 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:03:12 +00:00
747521c849
Fixed the simplest of typos.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@761 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 16:00:30 +00:00
e48078b476
Updated to reflect change to BasecallingReadModel constructor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:43:26 +00:00
505f588768
Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:38:51 +00:00
96e73e496a
Delete deprecated old-school traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@758 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 14:57:17 +00:00
b840dd1320
Added some code to change the instrumentation for tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@756 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 05:15:27 +00:00
6c5fbb988b
Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@754 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:09:20 +00:00
e293d65ede
Refactored to allow the user to specify the range of cycles they wish to call. Simply specify a single range (i.e. '0-75') or two ranges ('0-75,76-151'). This allows single and paired-end read processing to coexist happily. Also implements annotation of an aligned bam file (which should hopefully fit in under two gigs now, but I'm waiting on a bug fix or a clarification from the Picard team.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@753 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:07:24 +00:00
08c9f4d86b
Renamed to BasecallingTrainer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@752 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:03:46 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
40dbc21df7
Moved ParseException to it's own file and made it public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@750 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 14:42:44 +00:00
ff798fe483
Reintroduce support for interval-based traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 22:54:18 +00:00
3441795d9c
better handling of edge cases (zero coverage, reference mistakes, etc.)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@747 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 18:04:37 +00:00
7c615c8fb0
Some changes to the system for annotating a pre-aligned bam file. Doesn't fit within 2gigs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@746 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 17:42:08 +00:00
a39c8839c8
print percentage sign!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@745 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 14:38:20 +00:00
c10741e9f5
Rename TraverseLociByReference to TraverseLoci to represent its new function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@743 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 01:31:57 +00:00
e6ce80c8e3
Fix for GSA-44...don't throw exception when user specifies -h.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@742 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 00:42:00 +00:00
d35e20ce21
Better error checking for missing .dict file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@741 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 21:57:12 +00:00
7161b8f927
Disable support for short name values directly abutting their arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@740 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 16:09:32 +00:00
d152c2b911
New GATKArgumentCollection caused a subtle bug with argument grouping and the help system. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@738 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 14:54:25 +00:00
94e324b844
Write N for the alt allele when we're hom-ref.
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Stop EM loop when we've converged (likelihood[t-1] == likelihood[t]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@737 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 13:58:11 +00:00
bd53bc18f9
added new required annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 12:24:06 +00:00
28bf7ec8ad
Aesthetic cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@735 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 04:09:23 +00:00
a0464633fd
Whoops. Changed denominator from reads to bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@734 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:42:25 +00:00
5d60efc498
Factored out some simple stats accumulation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@733 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:37:57 +00:00
81fac73c01
LOD checks for normal and brute force versions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@732 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 02:56:03 +00:00
527df6e57b
Massive speed-up, clean-up and tabular output.
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This program is going to rule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@731 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 16:52:40 +00:00
3b57a35009
don't be tricked by multiple read groups with the same sample id!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@730 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:28:55 +00:00
947bac5cdc
vast speedup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@729 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:27:58 +00:00
6f1559bd77
Cleaned up a bit. Added some documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@728 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:22:24 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:02:12 +00:00
f33f3c0434
added LOD threshold for determining when to clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@725 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:23:59 +00:00
99d4ebc26d
Added functionality to return the final accumulator of a traversal, so external tools can get the result of a walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@724 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:20:27 +00:00
dae77bf14a
Fixed a typo in a comment.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@723 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:31 +00:00
bfc40f54f0
Nicer output when training off of perfect reads. Not that that works yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:08 +00:00
d1f3000afa
bed-style output for IGV
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@721 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 17:58:44 +00:00
36db44620b
Improved output. Can optionally limit the number reads actually called.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@720 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 00:07:57 +00:00
7834b969b4
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 23:20:11 +00:00
50f32b7f61
Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@718 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:20:18 +00:00
0f8e6061b6
Simple interface improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@717 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:08:09 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
67293168e7
Support periods in sequence names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@715 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 20:17:57 +00:00
641afc4e76
fix a crash in the event that the input file has no read groups!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:41 +00:00
d8c1b010f1
Fixing the naming of the function I checked in earlier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@713 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:10 +00:00
5858f20902
Documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:58:43 +00:00
68c9455c0f
Moved the base complement method to BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:57:48 +00:00
3761c0900b
Added Bustard vs. Four-prob percent bases consistent output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@710 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:01:41 +00:00
7a1f85ff86
option to print out the indels found by the cleaner to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:50:08 +00:00
b62bddee42
The header was never being set.
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Added this hack for now and will alert the authorities ASAP...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@708 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:18:51 +00:00
959cf09d4b
Removed some debugging print statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@707 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:12:42 +00:00
2f42a643a8
A new, much simpler (and now, complete) driver program for four-base probs. Serves as a model for anyone who wants to write their own driver program that trains and calls with data from a different source than the raw Illumina data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@706 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:58:22 +00:00
5824dea0c1
Trains and calls a read at a time rather than a base at a time (which, given it's name, it should have done in the first place)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@705 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:57:00 +00:00
e4770885fd
The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:55:49 +00:00
fdd123fe16
A parser the raw Illumina data. Allows one to arbitrarily jump from one tile to another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:53:07 +00:00
7aa90757ac
Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@702 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:18 +00:00
6d98234555
Holds raw intensities, sequence, and quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@701 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:03 +00:00
241de0b235
A class that implements multiple training strategies and presents the training data in a common form.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@700 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:51:29 +00:00
64c65c7751
New methods to generated compressed SQ quality elements in line with the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:50:31 +00:00
c3b2c66911
The GATK doesn't need the rest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@698 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:20:45 +00:00
0215905bb6
Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 15:17:32 +00:00
5dda448ae0
1. Add printouts for the cleaner
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2. First pass at the entropy interval walker (still needs work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@696 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:59:48 +00:00
80c13f7127
Added a getter for command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@695 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:55:52 +00:00
307c6e4ecf
Oops. Forgot to add new file to svn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@694 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 00:52:30 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
7b59f63f12
and don't forget to close sam writer after we are done...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@692 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:46:36 +00:00
de0cce87ea
new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:24:23 +00:00
12ae3a22b6
Break locus context data access providers into modular components in preparation for traverse by loci.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 18:51:16 +00:00
7084ecdeb6
a few changes; checked in to allow debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@688 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:50:48 +00:00
5b47c5ab6c
fixing kiran's busted build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 21:29:04 +00:00
4f2c8bf0a3
Fixed an import statement that broke when all the files were moved to this directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@685 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:43:16 +00:00
cedc4c9ccb
Refactored into oblivion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@684 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:33:07 +00:00
kiran
ebanks
andrewk
hanna
jmaguire
aaron
depristo
mmelgar
kcibul
asivache