4d75b26b7a
Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 06:17:31 +00:00
6dc1275cfb
Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3183 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-16 00:15:57 +00:00
f4673efd2f
Moving to archive as it's no longer supported
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:10:42 +00:00
02a6f4c401
Moving over to VariantContext
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:07:28 +00:00
7adff5b81a
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:36:19 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
ac6f6363ce
Execs() temporarily disabled after removal of bam file. New tests forthcoming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3178 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:11:56 +00:00
ac9dc0b4b4
Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:53:02 +00:00
3330e254a9
Standardize the dbsnp track name in preparation for case-sensitivity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:41:57 +00:00
5f7564bf0a
Better naming of output columns
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 18:08:07 +00:00
e682460c1f
add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 16:31:43 +00:00
b54031fc86
adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 06:09:27 +00:00
04909fa6ad
Removing arbitrary selects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 17:46:39 +00:00
f1189bac5a
Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 16:58:55 +00:00
b930dc52a5
Integration test for GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:43:25 +00:00
c0f4695902
Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:42:19 +00:00
74ec72d1ac
Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:39:50 +00:00
77a6608784
Changed a variable name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:38:18 +00:00
7b8056099c
Fixed 'N' reference-base handling, changed some comments, var names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:37:25 +00:00
dde092fb61
Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run.
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Heads up everyone: by default, *no* modules are run. Please add "-all" to your scripts to maintain the previous behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 22:15:58 +00:00
0b575596f8
Fix for concordance: samples found only in truth no longer kill it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 21:33:49 +00:00
8573b0bc6f
Refactoring intervals, separating the process of parsing interval lists,
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sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:50:38 +00:00
d0123956bc
Modified comments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:41:59 +00:00
7b05091c04
DoC now does not require a -o argument. (Change for Matt)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 13:58:17 +00:00
e413882302
Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 20:42:18 +00:00
14b8101d45
Error message fail. Failed to supply one of the valid interval file types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:19:01 +00:00
60d54e69f3
Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-12 01:11:27 +00:00
d06c7835d8
Adding performance tests for the indel realigner; should take ~3 hours.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 04:45:22 +00:00
3434a61146
Don't trigger when ref=N (which can happen when a dbsnp track is provided)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 02:59:11 +00:00
961ca05abc
Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-11 01:43:07 +00:00
fa01876255
UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 19:42:29 +00:00
0cc6d0fbbb
One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:48:36 +00:00
c2a37e4b5c
Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:36:06 +00:00
71f38a9199
Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests).
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Should take ~3 hours to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 18:30:59 +00:00
e73e6a4fb0
Significant memory improvements to plink code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 16:12:38 +00:00
f1b1e70612
Bug fix for multisample calls in ApplyVariantClusterWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 12:01:15 +00:00
3f2455e346
Better error message as suggested by James P
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:52:53 +00:00
fba48b515a
Heads up everyone:
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For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:37:25 +00:00
e286623f6f
Use byte[] instead of String in an attempt to cut down on memory usage
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 05:32:54 +00:00
7025f5b51d
Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 19:37:17 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +00:00
4014a8a674
A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.
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Thanks!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 06:14:15 +00:00
e148a3ac61
added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option.
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Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 05:14:41 +00:00
20cc2a85a4
removed the hashmap from Genotype Concordance, moved it into a table
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 21:24:48 +00:00
e55f27b3b1
forgot a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:51:13 +00:00
9ca8e345fc
by-by old junk.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:41:48 +00:00
8fd59c8823
Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 20:39:55 +00:00
918b746798
More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 16:38:28 +00:00
e7dad728df
Trivial output changes for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 14:47:43 +00:00
058e7d3d12
Bug fix for Gregory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 00:21:35 +00:00
aaron
asivache
ebanks
chartl
weisburd
hanna
rpoplin
depristo