1de713f354
Massive review of maybe 50% of the exceptions in the GATK. GATKException is a tmp. tracker so that I can tell which StingExceptions I've reviewed. Please don't use it. If you are working on new code and are considering throwing exceptions, it's either UserError or StingException, please
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4246 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 23:21:17 +00:00
a47824d680
A couple of type specific implementations of a single extend() method: takes an array (byte[] or short[] currently) and "extends" it to the left or to the right by the specified number of elements. Returns newly allocated array, with the content of original array copied in (if we extend by n elements to the left, then the returned array will have n default-filled elements *followed* by the content of the old array).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3932 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 15:30:48 +00:00
dfc36c1e95
Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 22:12:25 +00:00
727822adb4
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:05:13 +00:00
2f3933148d
Added fast split(str, delimiter) methodf
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 03:37:26 +00:00
8b2ce128b5
Optimized the join(..) method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:55:07 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
47e30aba92
Rods for reads hooked up into the cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 18:17:56 +00:00
076d21d394
Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3054 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-22 02:47:09 +00:00
934d4b93a2
VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 19:02:25 +00:00
af8c47fc2f
Fixing up testVariantContext for integration tests for variant context. Printing of VCs and genotypes now stable using sorting. Cleaned up comments in quality score by strand. RefMetaDataTracker now directly allows walkers to obtain VariantContexts using the simple Collection<VariantContext> getAllVariantContexts(GenomeLoc curLocation, EnumSet<VariantContext.Type> allowedTypes, boolean requireStartHere, boolean takeFirstOnly) function. VCF and dbSNP VariantContexts now officially supported. Other importan types can be added to the adapator system in refdata package. Integration tests later today
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2791 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 15:42:54 +00:00
9a658e6b18
-Fixed VCF header line bug
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-Added useful trim() method for Strings for characters other than whitespace
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2538 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-07 17:51:41 +00:00
e793e62fc9
minor code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2189 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:57:20 +00:00
be6a549e7b
Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:34:48 +00:00
aece7fa4c7
a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2057 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 16:50:01 +00:00
4558375575
Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.
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VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper. UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).
This is a fairly all-encompassing check in. It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout. All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.
Stage 2 of the process will happen later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 02:41:20 +00:00
ad1fc511b1
intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1903 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 06:31:15 +00:00
52d2e0ca07
All walkers now use read.getReadGroup()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1839 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 19:27:40 +00:00
d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
ccdb4a0313
General-purpose management of output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
4efe26c59a
Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found.
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Minor: refactor 454 filtering
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1300 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 19:53:51 +00:00
b18caa2052
Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1225 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 20:42:12 +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
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
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
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
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
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
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
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
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
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
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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could be extracted to a char[] containing the reference bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:45:11 +00:00
e848f34896
countOccurances of char in string and max of a list of bytes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@622 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:49 +00:00
6cef8bd76c
added k-best quality path enumeration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@497 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 20:26:51 +00:00
af6788fa3d
Misc:
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1. Added logGamma function to utils
2. Required asserts to be enabled in the allele caller (run with java -ea)
3. put checks and asserts of NaN and Infinity in AlleleFrequencyEstimate
4. Added option FRACTIONAL_COUNTS to the pooled caller (not working right yet)
AlleleFrequencyWalker:
5. Made FORCE_1BASE_PROBS not static in AlleleFrequencyWalker (an argument should never be static! Jeez.)
6. changed quality_precision to be 1e-4 (Q40)
7. don't adjust by quality_precision unless the qual is actually zero.
8. added more asserts for NaN and Infinity
9. put in a correction for zero probs in P_D_q
10. changed pG to be hardy-weinberg in the presence of an allele frequency prior (duh)
11. rewrote binomialProb() to not overflow on deep coverage
12. rewrote nchoosek() to behave right on deep coverage
13. put in some binomailProb() tests in the main() routine (they come out right when compared with R)
Hunt for loci where 4bp should change things:
14. added FindNonrandomSecondBestBasePiles walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@471 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 15:35:07 +00:00
df5aae5ed4
got read of a couple of warnings and added percentage(x,base) methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@462 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 15:15:21 +00:00
72a3d84ed2
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:13:10 +00:00
998fad76c6
Some utility methods for creating pileups of secondary bases and secondary quals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@397 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:57:54 +00:00
bb666ce392
Added mappingQualPileup function for use in the verbose mode of Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:51:26 +00:00
f39092526d
Added function RandomSubset
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@379 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:14:53 +00:00
00722e19bc
The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@319 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:19:54 +00:00
3f75fc4e83
Unfortunately, because BWA occasionally outputs crazy reads, we need
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to make sure not to have an ArrayIndexOutOfBoundsException thrown.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@297 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 03:51:35 +00:00
42eb356782
1. modifed by read traversals with indexes to be more general
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2. GenomeLocs for reads should have ends spanning the read
(moved it to GenomeLoc from Utils)
3. Got rid of those stupid unmappable characters from comments in various files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 18:24:08 +00:00
d952790258
GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 22:54:38 +00:00
385736469c
High performance pileup code and utilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 00:47:47 +00:00
d7c0bcc223
Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.
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All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-28 20:37:27 +00:00
230c1ad161
moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@211 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 14:02:55 +00:00
d11bb0fc64
Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@187 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:17:38 +00:00
depristo
asivache
weisburd
hanna
ebanks
aaron
jmaguire
kiran