8f2bfac7a6Bug fix for NullPointerException
ebanks
2010-04-26 05:02:09 +0000
f5a3b128c8Fixing bug that's not caught by integration tests: If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics. Instead, just check that any eval's no-call count is 0.
ebanks
2010-04-26 02:40:34 +0000
29ab59a7b3Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null
depristo
2010-04-24 21:31:03 +0000
c8d09a29edsome quick changes to the VE output system - more to come.
aaron
2010-04-23 21:55:08 +0000
7f4d5d9973Ti/Tv by AC
depristo
2010-04-23 17:56:29 +0000
42bcca1010Pulling out the left-alignment code for indels so that other walkers can use it.
ebanks
2010-04-23 16:12:34 +0000
10bcd725931st attempt to implement extra columns
weisburd
2010-04-23 15:49:37 +0000
a72a5a7b1aData object for representing a single amino acid
weisburd
2010-04-23 15:49:06 +0000
e7c0ded40eFixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
rpoplin
2010-04-23 15:48:41 +0000
e0b51d0df0Trigger cleaning of duplicate reads. Also beeter debug output.
ebanks
2010-04-23 15:12:28 +0000
3adf7fbf64bug fix for known-indels used as consenses
ebanks
2010-04-23 13:52:51 +0000
f050beada6make sure we do delete the temp file we create
aaron
2010-04-23 05:32:49 +0000
536f22f3bdadding VC adaptor for GELI, along with unit tests.
aaron
2010-04-23 05:28:39 +0000
3d2c836db6Bug fix for case sensitivity
depristo
2010-04-23 03:08:58 +0000
8c94df6f00Bug fix for Chris: deal with sites that have "semi-deletions"
ebanks
2010-04-22 18:34:41 +0000
e643a9e7a5Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
weisburd
2010-04-22 12:11:19 +0000
653e08c0b6Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position).
weisburd
2010-04-22 12:11:03 +0000
32d86cf457Rev the reservoir downsampler to support partitioning through a functor.
hanna
2010-04-21 19:50:26 +0000
ef6d900eb8for now, set log error to -1
asivache
2010-04-21 19:21:06 +0000
e9e844fbf51. Reverting: dbsnp automatically is a comp 2. Fixing logic for min Qscore calculation
ebanks
2010-04-21 18:51:35 +0000
532263ea25Oooops, forgot to update the test
asivache
2010-04-21 18:38:24 +0000
1373fee278Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change.
asivache
2010-04-21 18:19:03 +0000
ab34397d2eContinuing to stamp out the non-ASCII copyright virus.
hanna
2010-04-21 14:50:45 +0000
84f1ccd6acTwo dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations).
chartl
2010-04-21 14:04:10 +0000
2fdc1cf490Bed ROD track support
depristo
2010-04-21 13:22:42 +0000
51b3998082deleting unused code from VariationFiltration
depristo
2010-04-21 13:22:19 +0000
4abd3b0b7bFixing known/novel calc now that dbsnp isn't a default comp track
ebanks
2010-04-21 05:43:59 +0000
114819d980Allow user to set min confidence score for comp tracks too
ebanks
2010-04-21 05:09:09 +0000
3db73e0791Renaming for consistency
ebanks
2010-04-21 03:00:43 +0000
3b5673d9671. Removed -all; by default all modules are used; use -none for no modules. 2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason. 3. Cleaned up dbsnp module output to print the right numbers.
ebanks
2010-04-21 02:46:42 +0000
4e18c54bb8fixing a couple of commented out portions of the VCFReader test
aaron
2010-04-20 22:20:35 +0000
6fda78f93fAlways return deleted bases in upper case
asivache
2010-04-20 19:17:40 +0000
52a570637dAlways keep event bases in upper case
asivache
2010-04-20 19:16:39 +0000
80c4f88a72removing the Variation interface.
aaron
2010-04-20 18:56:45 +0000
cdc175f7e3Synchronizing version to make sure everything compiles; this model is not operational yet
asivache
2010-04-20 17:41:52 +0000
4437456bb5Pass array of ref bases to callExtendedLocus()
asivache
2010-04-20 17:41:13 +0000
5d2fab93f4Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base.
asivache
2010-04-20 17:40:30 +0000
01e6492ba9Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday
asivache
2010-04-20 17:38:09 +0000
4723cad1beNew method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase())
asivache
2010-04-20 17:35:09 +0000
cac125b35cFixed incorrect symbol printed into the output file (tag had 'R', should have had 'T')
asivache
2010-04-20 16:37:28 +0000
124b7a2a58Moved ApplyVariantClusters over to VariationContext
rpoplin
2010-04-20 16:20:25 +0000
cc3061538fAdding a license to the root directory in case BOSC checks for one. Has the added bonus of boosting my svn stats.
hanna
2010-04-20 16:04:29 +0000
546dfb629eA draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :)
asivache
2010-04-20 15:38:16 +0000
c1e53d407dThe copyright tag that I copied/pasted from a LaTeX document into IntelliJ had unicode quote characters embedded in it. These characters were invisible inside IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason have a different default charset. Fixed.
hanna
2010-04-20 15:26:32 +0000
b5f6f54968Almost done removing any trace of the old Variation and Genotype interfaces.
aaron
2010-04-20 14:52:15 +0000
7902db616eMarginally more useful output
depristo
2010-04-20 14:45:14 +0000
818a95ea6eTest of new copyright message without unicode characters.
hanna
2010-04-20 14:14:54 +0000
00feb3eee0Moving over to VariationContext in CountCovariates. Removed references to class Variation.
rpoplin
2010-04-20 13:26:22 +0000
1bc26f69e9An attempt to cleanup the Utils directory. Email to follow.
hanna
2010-04-19 23:00:08 +0000
c08936d6f4Added a reservoir downsampler which can sample elements in an iterator uniformly from a stream (see Vitter 1985). Thanks to Eric and Andrey for the pointer.
hanna
2010-04-19 20:48:14 +0000
c44f63c846Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch.
ebanks
2010-04-19 14:28:12 +0000
abf48cee05Moving over to VariantContext from Variation
ebanks
2010-04-19 06:56:29 +0000
d73c63a99aRedoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
ebanks
2010-04-19 05:47:17 +0000
4eba9bffc1Grabs average SNP calls, mismatch rate, aligned reads, and other important lane metrics from a SQUID export and summarizes them across multiple margins (lane numbers, flowcells, samples, libraries)
chartl
2010-04-17 03:09:05 +0000
131703d9dbmore clean-up: moving AlleleBalanceInspector to archive.
aaron
2010-04-16 20:53:33 +0000
534f24177aMove to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker.
ebanks
2010-04-16 20:09:48 +0000
8c32bb8f0aComplete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code)
ebanks
2010-04-16 19:41:42 +0000
e11ca74eb5removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext.
aaron
2010-04-16 18:59:29 +0000
d5e5589b8fNo longer used
ebanks
2010-04-16 17:57:39 +0000
be7cbf948badding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests.
aaron
2010-04-16 17:41:48 +0000
bbb83859cdAdding VE modules to package
ebanks
2010-04-16 14:44:06 +0000
4d75b26b7aRemoving 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.
aaron
2010-04-16 06:17:31 +0000
6dc1275cfbUtility 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 :)
asivache
2010-04-16 00:15:57 +0000
f4673efd2fMoving to archive as it's no longer supported
ebanks
2010-04-15 22:10:42 +0000
02a6f4c401Moving over to VariantContext
ebanks
2010-04-15 22:07:28 +0000
7adff5b81aRenaming for consistency
ebanks
2010-04-15 20:36:19 +0000
e702bea99fMoving VE2 to core; calling it "VariantEval" (one more checkin coming)
ebanks
2010-04-15 20:25:47 +0000
ac6f6363ceExecs() temporarily disabled after removal of bam file. New tests forthcoming.
chartl
2010-04-15 20:11:56 +0000
ac9dc0b4b4Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
ebanks
2010-04-15 19:53:02 +0000
3330e254a9Standardize the dbsnp track name in preparation for case-sensitivity
ebanks
2010-04-15 19:41:57 +0000
5f7564bf0aBetter naming of output columns
ebanks
2010-04-15 18:08:07 +0000
e682460c1fadd 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.
aaron
2010-04-15 16:31:43 +0000
b54031fc86adding 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.
aaron
2010-04-15 06:09:27 +0000
2ca1849df9Adding HaplotypeScore to the VariantAnnotator package (so it can be used with Firehose)
chartl
2010-04-14 18:37:21 +0000
2e4377b1cfAwesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
chartl
2010-04-14 18:17:41 +0000
f1189bac5aBug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0)
ebanks
2010-04-14 16:58:55 +0000
b930dc52a5Integration test for GenomicAnnotator
weisburd
2010-04-14 14:43:25 +0000
c0f4695902Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files.
weisburd
2010-04-14 14:42:19 +0000
04c22a6640Added handling of UCSC and NCBI reference sequences
weisburd
2010-04-14 14:40:31 +0000
74ec72d1acAdded AnnotatorROD - the TabularROD format specific to GenomicAnnotator
weisburd
2010-04-14 14:39:50 +0000
77a6608784Changed a variable name
weisburd
2010-04-14 14:38:18 +0000
7b8056099cFixed 'N' reference-base handling, changed some comments, var names
weisburd
2010-04-14 14:37:25 +0000
dde092fb61Added 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. Heads up everyone: by default, *no* modules are run. Please add "-all" to your scripts to maintain the previous behavior.
ebanks
2010-04-13 22:15:58 +0000
0b575596f8Fix for concordance: samples found only in truth no longer kill it.
ebanks
2010-04-13 21:33:49 +0000
8573b0bc6fRefactoring intervals, separating the process of parsing interval lists, 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.
hanna
2010-04-13 15:50:38 +0000
ebanks
depristo
aaron
weisburd
rpoplin
chartl
hanna
asivache