7008a469dcUpdate MalformedReadFilter to pass reads that have cigar strings like 40S36I that have 0 aligned bases in the genome. We'll have to fix walkers as faults appear.
hanna
2010-10-11 03:01:04 +0000
530875817fExperimental code for better filtering of bases in sam records. Not hooked up yet.
ebanks
2010-10-11 02:19:51 +0000
0a4cf02a52Fix for index out of bounds exception in VR.
rpoplin
2010-10-10 17:35:15 +0000
116309b3c3More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI
depristo
2010-10-08 20:22:12 +0000
38a67fed63High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.
depristo
2010-10-08 19:53:21 +0000
6368a46babScala protected is more akin to Java private than Java protected. Not typing these defs.
chartl
2010-10-08 19:36:23 +0000
bdd3a9752eChanged min MQ and BQ to 20 (for phasing)
fromer
2010-10-08 19:27:45 +0000
05500d1a8dAn iterator wrapper/adapter: takes GenomeLoc iterators 1 and 2 and traverses intersections of intervals from 1 with intervals from 2. Both 1 and 2 must be SORTED and NON_OVERLAPPING, but this iterator does NOT perfrom any checks, so if these conditions are not met, the behavior is unspecified
asivache
2010-10-08 16:34:00 +0000
253d528e49not ready for commit yet
asivache
2010-10-08 15:30:55 +0000
4f2f33b42afix method invocation to conform to new API; this version of the code will compile but new functionality is still not fully in
asivache
2010-10-08 15:30:26 +0000
cece19d4d2not ready for commit yet
asivache
2010-10-08 15:14:54 +0000
b3d81984aarenaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
asivache
2010-10-08 14:10:11 +0000
77dddd0afarenaming MergingIterator to RODMergingIterator as it is more appropriate for this specialized implementation
asivache
2010-10-08 14:08:28 +0000
bffb8bb01fThe SVN repository is not for dumb analysis-specific scripts.
chartl
2010-10-08 14:04:53 +0000
21ec44339dSomewhat major update. Changes:
chartl
2010-10-08 13:30:28 +0000
e02f837659Added the ability for Queue functions like mkdirs to override if they are done or not.
kshakir
2010-10-08 06:39:55 +0000
acd238f3f2For Chris: pull out the chromosome counting code into VCUtils so that other tools can make use of it. Transitioned SelectVariants over to use it.
ebanks
2010-10-08 04:37:54 +0000
3838823262Two ugly hopefully temporary fixes for new genotyping model: a) In Indel genotyper: we can't deal yet with extended events correctly and we are still triggering at each extended event which results in repeated records on a vcf. So, to avoid this, keep track of start position of candidate variantes we've visited and if we've visited a variant before we don't do it again. b) Avoid infinite terms in QUAL and in genotype likelihoods which can happen if posterior AF happens to be exactly zero. For now, hard-code a minimum value of each term of the posterior AF likelihood to be -300 (ie 1e-300 in lin space). This can be solved with better and smarter log-to-lin conversions and some precision fixes in AF calculation.
delangel
2010-10-08 00:53:16 +0000
0a2e76e9dc2nd step towards on the fly indexing. Also fixed parsing bug for headers with < symbols
depristo
2010-10-07 21:38:46 +0000
7bb9704592Update the BeagleOutputToVCF integration test because of removing the source header line. Source headers are provided by the engine for all VCF files now.
rpoplin
2010-10-07 19:55:57 +0000
7f25019f37Inprocess functions by default now log what output files they are running for. On -run cleaning up .done and .fail files for jobs that will be run. Added detection to Firehose YAML generator shell script for (g)awk versions that ignore "\n" in patterns. Removed obsolete mergeText and splitIntervals shell scripts.
kshakir
2010-10-07 19:08:02 +0000
0de658534dRemoved the qScale arguments in VariantRecalibrator. It is smarter about how it tries to find a cut so the arbitrary scale factor hopefully is no longer necessary. Now the recalibrated variant quality score more accurately reflects our believed lod of the call.
rpoplin
2010-10-07 18:04:57 +0000
ee00dcb79d1. Phasing now ignores bases without minimum base quality (BQ) and minimum mapping quality (MQ); 2. The probability of a non-called base is now divided by 3, to evenly split up the error probability over the non-called bases
fromer
2010-10-07 17:40:59 +0000
6205910f9fupdating integration test for Sarah Calvo
ebanks
2010-10-07 04:03:37 +0000
db47230dd9Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster. Shell invoking scripts so that even really long shell scripts make it through LSF. Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs. Switched the default from re-running everything to re-running only files that need to be regenerated. --skip_up_to_date replaced with --start_clean for those who want to regenerate everything. Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions. (40s for a 100 function graph exploding to a 2500 function graph)
kshakir
2010-10-07 01:19:18 +0000
04b4adafdaFile reports are now sorted in order
depristo
2010-10-06 21:54:23 +0000
652a3e8de5Added integration tests for ReadBackedPhasing
fromer
2010-10-06 20:50:32 +0000
f8f1cc45a3Now ReadBackedPhasing caps Base Quality by Mapping Quality
fromer
2010-10-06 20:48:57 +0000
bda427f078Change specification of AnnotationInputTable, and fix 2 bugs.
scalvo
2010-10-06 20:46:09 +0000
b5c127e643Removed HAPLOTYPE_STRAND_COLUMN; Previously, GenomicAnnotation allowed a user to specify the strand of the haplotypeAlternate, and would reverseComplement the haplotypeAlternate if HAPLOTYPE_STRAND_COLUMN was "-". The new specification does not allow this functionality, and instead requires both the reference and the alternate haplotypes to be on the + strand (as in VCF format).
scalvo
2010-10-06 20:37:41 +0000
ca5db821ceAdded the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality. Queue now submits new LSF jobs only after previous functions have completed successfully. When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs. Ported commands like creating directories and scatter/gather interval list to scala functions. Updates to LSF status tracking by porting the python to internally generated bash scripts. Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option? Changed BaseTest to allow scala to access paths to references. Changed the extension generator to default the analysis name to the walker "name".
kshakir
2010-10-06 18:29:56 +0000
3c5dc675abFor Guillermo: only decide that something is a clear reference call if it is at least 10 times as likely as the next best genotype
ebanks
2010-10-06 15:16:41 +0000
effcd26977Shorter outputs, new summary mode
depristo
2010-10-06 14:34:50 +0000
d841f260ebminor improvements to queue status
depristo
2010-10-06 14:34:35 +0000
0508dd0c31Better reporting -- figured out how to drop unused levels in subset
depristo
2010-10-06 14:31:51 +0000
00491fcd2eOnly see not writing GATK Run Report if you are running with debug enabled
depristo
2010-10-06 14:09:21 +0000
69485d6a7aAdded command line argument for the max value of the allele count prior in VariantRecalibrator (--max_ac_prior). Default value increased to 0.99 from 0.95.
rpoplin
2010-10-06 14:00:53 +0000
3d564f4a29reverting an accidental change from the dindel merge
ebanks
2010-10-06 03:08:09 +0000
28ac1d325eCommit for Ryan
chartl
2010-10-05 19:04:10 +0000
e8af776b99Fixes for example bam files
depristo
2010-10-05 18:43:02 +0000
b5e148140bOfficially fixed the UG priors; updated the default min MQ/BQs to pipeline values of q20 and min calling threshold to Q50
ebanks
2010-10-05 18:35:36 +0000
c6668bd49cFixed bug in phasing, where mapping probability was incorrectly raised to the power of number of non-null bases [instead, it is just multiplied into phasing probability once]
fromer
2010-10-05 17:07:31 +0000
250c18e679Error message fixes for the following issues:
hanna
2010-10-05 03:37:13 +0000
e340be34d8upping mem limit since something was unhappy with the lower limit
corin
2010-10-05 02:38:17 +0000
bb44044ce0Fixed re-builds of queue so that previously compiled classes are included. Fixes redundant case of "ant queue test" vs. "ant test". Refactored temp directory utils.
kshakir
2010-10-04 21:12:07 +0000
4dfed62e7dGenerating the Queue GATK extensions using java, then compiling all the Queue scala code at once to allow circular dependencies between existing and generated scala code. Will see how this behaves for those using IntelliJ as generated source code will disappear during an ant clean.
kshakir
2010-10-04 19:38:29 +0000
24cf6f9e36Fix to handle situation where there are no filtered variants.
kiran
2010-10-04 18:34:01 +0000
aa00801108remove reference to -mrl
ebanks
2010-10-04 17:27:01 +0000
0eb777612aSwap "." over to VCFConstants.MISSING_DEPTH_v3
chartl
2010-10-04 13:41:41 +0000
74087c44aeFixed a bug which caused a parsing exception when there was a variant with a dp field of ".", e.g. "GT:DP 0/1:." -- which can happen when using imputation.
chartl
2010-10-04 12:37:36 +0000
6448753cf7Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.
ebanks
2010-10-04 02:11:38 +0000
a15757b8e8Obsoleted by VariantReport.R
kiran
2010-10-04 01:00:59 +0000
cf01f6d58aRenamed conflicting 'package.dir' in build.xml to 'package.xml.dir'.
kshakir
2010-10-04 00:46:47 +0000
62f5383859* Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps:
kiran
2010-10-04 00:27:59 +0000
d8db48204eFix typo and tell people not to post user errors
ebanks
2010-10-03 18:58:03 +0000
490e5e1b0fBetter error when bad ref bases are provided
ebanks
2010-10-03 05:40:37 +0000
40b2f62a83Changed precision on Ti/Tv in venn diagrams
kiran
2010-10-02 05:27:13 +0000
d0e44b7a8eLower precision on Ti/Tv in variant summary matrix
kiran
2010-10-02 05:18:48 +0000
6deb755164Ti/Tv plots are restricted to a Ti/Tv range of 0.0-4.0. Added column to variant summary specifying the total variant counts (known+novel). Allele spectrum plots now show neutral expectation.
kiran
2010-10-02 05:15:34 +0000
64b7b3f83bfix for a recent change to the indexing code where we ignore the results of locking the file (this is bad), and as a result don't write the index; this should fix the build.
aaron
2010-10-02 04:35:11 +0000
7551ba8249Trival refactoring in preparation for on-the-fly indexing
depristo
2010-10-01 22:32:59 +0000
399e6f1463Make package dir configurable.
hanna
2010-10-01 22:25:17 +0000
1d7e48c4b0Venn diagrams are now oriented properly when a < b. Added a slide with callset summary table. All plots now show the present-in-a, filtered-in-b metrics. Added title page with project name, author, and timestamp.
kiran
2010-10-01 22:17:21 +0000
2f7892601cUseful debugging argument added to VariantRecalibrator to only use sites whose qual field is above --qual
rpoplin
2010-10-01 21:08:55 +0000
575c38fc04Accidental fail to commit missing file.
hanna
2010-10-01 20:26:51 +0000
fe29c8b09cPlaceholder commit: improvements to VariantReport (now shows stats for variants that are called in one set and filtered in another). Better command-line argument support.
kiran
2010-10-01 18:46:53 +0000
d4398f2686silly bug fix: if I'm to do a short term hack to avoid -infinity likelihoods I might as well do it right.
delangel
2010-10-01 18:39:45 +0000
8d25a5f9f2A mechanism for supplying attribution text -- mainly useful for external walkers.
hanna
2010-10-01 18:31:19 +0000
e920badcc4Temporary fix for case where genotype likelihoods are exactly (1,0,0) or (0,1,0) etc. at a site with new indel genotyper: this would make us blow up when converting to log space and try to assign genotypes at a site. A more robust solution is in the works.
delangel
2010-10-01 17:43:43 +0000
b83fdf8a17Bug fix in AnalyzeAnnotations. Be sure the site is a biallelic, unfiltered SNP.
rpoplin
2010-10-01 13:09:46 +0000
7639692e5bSigh. Fix the source of even more UserErrors in the phone home directory: make sure to gunzip the beagle files before passing them into the conversion walker...
chartl
2010-10-01 03:28:36 +0000
fa9c21c020More fixes for exact AF calculation model in new unified genotyper: a) Fixed bugs in new dynamic programming-based genotyper b) Fixed up temp hack that handles extended pileups for now.
delangel
2010-10-01 02:32:50 +0000
eb67aee732bug fix: forgot to uncomment code to compute genotype likelihoods
delangel
2010-09-30 21:38:22 +0000
ece694d0afNext iteration on new UG framework: - Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2. - Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper. - Integrated and added new Dindel likelihood estimation model. - Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup.
delangel
2010-09-30 21:33:59 +0000
027241e1caMoved the test classes from java/classes/testclasses to java/testclasses. Update your IntelliJ settings!
kshakir
2010-09-30 20:42:41 +0000
4ea73bcfb1Basic unit tests for WalkerManager.
hanna
2010-09-30 19:27:41 +0000
bf7fd08810Fix newly-introduced bug in the PluginManager/DynamicClassResolutionException where, when the system can't find a plugin of the correct name, the system prefers to crap all over itself and throw an unintelligible NullPointerException rather than displaying an intelligent error.
hanna
2010-09-30 19:07:05 +0000
14e19f4605(Slightly) better exception text when SAM/BAM output file can't be created.
hanna
2010-09-30 18:43:22 +0000
1fb8c86f6dLooks like we've got two competing models for an empty interval list: null and the empty list. Score another victory for the integration tests.
hanna
2010-09-30 17:11:47 +0000
78343be52cAt some time in the recent past, we lost our ability to process the '-L all' argument. Brought it back, and added an integrationtest to make sure it stays around.
hanna
2010-09-30 15:58:43 +0000
f34b4c6b82Be smarter if the beagle output is set such that getParent() returns null. Up the memory limit.
chartl
2010-09-30 12:48:47 +0000
0142047da9And a bugfix 3 seconds later. Don't tell java to use up to 20g while telling the farm to kill the job if it tries to exceed 4g.
chartl
2010-09-30 02:08:47 +0000
06970ae039A qscript that refines genotypes with beagle and merges them into one vcf (running currently on the recent chr20 production calls).
chartl
2010-09-30 02:05:30 +0000
e80742e72fUse -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)).
delangel
2010-09-29 22:46:39 +0000
732aa32758Every Sting app from now on will be forced into the US English locale.
hanna
2010-09-29 21:55:21 +0000
20ffe484bcAdded detection and INFO field marking of phasing inconsistencies (and optional filtration using --filterInconsistentSites)
fromer
2010-09-29 19:28:56 +0000
a6c7de95c8By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout.
rpoplin
2010-09-29 18:56:50 +0000
2d1265771fFix for G: make sure to generate the genotype conformations in the grid for the target frequency when not using grid search for anything except the conformations
ebanks
2010-09-29 16:44:53 +0000
4556e3b273First iteration in filling up exact AF calculation with new refactored UG. Code computes EM iterations of exact AF spectrum and returns to caller.
delangel
2010-09-29 16:21:54 +0000
2708e83198For show (Queue works nicely): An analysis script that runs QC for the omni chip
chartl
2010-09-29 15:04:17 +0000
0d71dff928Small bug fix to the new UG (need to initialize the entire posteriors array) means that we also get identical results as old UG when calling with 60 samples in the pilot1 data. Now that I'm happier with UGv2, I've transitioned it to use the correct AF priors instead of the busted ones still in the old UG.
ebanks
2010-09-29 14:24:50 +0000
eee134baf2Chris found a bug in the downsampler where, if the number of reads entering the pileup at the next alignment start is large, we don't add as many of those incoming reads as we should. No integration tests were affected.
hanna
2010-09-29 11:18:12 +0000
0ec07ad99aInitial version of refactored Unified Genotyper. Using SNP genotype likelihoods and GRID_SEARCH AF estimation models, achieves the exact same results as original UG on 1-2 samples with the exception of strand bias (not implemented yet); other than that I have no idea. Needs tons more testing. Do not use. For Guillermo only.
ebanks
2010-09-29 08:42:25 +0000
6df7f9318fFor enums generate the full path to the Enum type to avoid collisions such as enum Model and enum Model used in the same class.
kshakir
2010-09-29 05:28:59 +0000
hanna
ebanks
rpoplin
depristo
chartl
fromer
asivache
kshakir
delangel
scalvo
corin
kiran
aaron