08c4fb86e3
Derive examples from real data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1213 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 04:21:37 +00:00
03e1713988
Better support for specifying read filters to apply directly from the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 23:59:53 +00:00
ce08f5f0c3
Removed some unused variables, fixed some javadoc. The usual.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1211 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 22:10:22 +00:00
9cfd89c54f
a small refactoring, and some documentation cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1210 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 22:03:45 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
3519323156
Output the correct geli text format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1208 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 19:45:18 +00:00
99631cdaa1
fix and then deprecate the rodGELI class (GELIs suck)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1207 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 19:18:13 +00:00
60a86fb34a
Better handling of fasta files with non-standard extensions.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1206 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 18:18:48 +00:00
5e26770634
Hack the MicroScheduler to be tolerant of RefWalkers. We need to implement a longer-term solution to make it easier for datasources to report problems they've encountered along the way (GSA-103).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1205 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 17:26:59 +00:00
bc44e08225
refactored output logic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1204 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 16:13:01 +00:00
3fe7104963
Added walker to filter out clustered SNPs from a call set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1203 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 03:16:27 +00:00
8ee5c7de8e
GLF reader and writer check in.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1202 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 23:06:37 +00:00
c8fcecbc6f
Added ParseDCCSequenceData.py to repository and made changes that allow an analysis of quantity of sequence data by platform and project, moved table / record system to a new module called FlatFileTable.py and built that into ParseDCCSequenceData and CoverageEval.py; changed lod threshold in CoverageEvalWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1201 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 22:04:26 +00:00
3f0304de5a
Get rid of unused iterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1200 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:39:16 +00:00
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
aacec3aeb0
rod for binary GELI files (still needs to be tested)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1198 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:25:56 +00:00
e106cf73d8
A quick change to provide more verbose output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1197 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 19:08:19 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
0a67386525
.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1195 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:59:36 +00:00
d8fbb2b62c
Refactoring; make a better home for the MalformedReadFilteringIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:54:20 +00:00
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
1d84c9da96
sortByRef now supports x:y location syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1186 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 16:42:40 +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
f5b00c20d0
Updated python files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 14:15:39 +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
hanna
aaron
ebanks
kcibul
andrewk
jmaguire
kiran
depristo
mmelgar