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1054 Commits (79c4cc1db7ac3da56db8e039a76c75b6836d61be)

Author SHA1 Message Date
ebanks 4d9c826766 Integration tests actually run on real data now. 
<tries to hide sheepish grin>


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2061 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 21:04:14 +00:00
ebanks a048f5cdf1 -Refactored JointEstimation code so that pooled calling will work 
-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-17 20:21:15 +00:00
asivache 21729d9311 Do not print debug message when debug mode is not requested!! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2056 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 20:28:41 +00:00
rpoplin 967215066d The old CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2055 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 19:16:46 +00:00
ebanks 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. 
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
kiran 103763fc84 An accessor for the VCF header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2051 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-15 09:28:25 +00:00
ebanks bf451873ff 1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction 
2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 18:02:18 +00:00
asivache 1be36ca959 Bug fix: when cleanedReadIterator is initialized, it gets immediately set to the contig of the first cleaned read; when the first uncleaned read coming in is on the lower contig, this would trigger 'readNextContig' with that lower contig as an argument. As the result, the whole cleaned reads file would be read through the end and no cleaned reads would be ever seen by the code afterwards. Now we do not call readNextContig if the (uncleaned) read's contig is lower than the current contig already loaded into cleanedReadIterator. the 'readNextContig' method now also throws an exception if requested contig is less than the currently loaded one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2037 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 15:41:26 +00:00
depristo cff31f2d06 comments for eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2035 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 14:19:31 +00:00
aaron 234bb71747 changed the toVariation() method to take a reference base, instead of using the reference base loaded from the underlying data source (if it was reference aware). Also changed some isVariant() methods which weren't using the passed in ref base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2034 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 06:54:38 +00:00
ebanks 902cf84448 Bug fix: if the most likely allele frequency is 0, don't make a variant call (even if the Qscore for AF=1/n > threshold) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2033 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 04:10:32 +00:00
ebanks 555fb975de 1. Print out allele frequency range (from joint estimation model only). 
2. Don't print verbose output from SLOD calculation (it's just a repeat of previous output).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2032 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 03:59:13 +00:00
hanna 8145ed4672 Take 2, updating picard with bug fix for bam files containing no reads. 
Just stomped on the existing md5s because that's what Eric told me to do.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:52:08 +00:00
ebanks 61b5fb82ce 2 major changes: 
1. Add dbsnp RS ID to VCF output from genotyper; to do this I needed to fix the dbsnp rod which did not correctly return this value.

2. Remove AlleleBalanceBacked and instead generalize the arbitrary info fields backing VCFs (and potentially others) in preparation for refactoring VariantFiltration next week.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2028 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 22:51:49 +00:00
aaron c3c001e02e cleanup of the traversal output code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 06:18:10 +00:00
ebanks 0922400ca9 Don't try to calculate ratios when DoC is zero (which happens when calls are made by an LD-aware genotyper) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2025 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 02:51:44 +00:00
hanna 2ea85fb62b Fix some problematic command-line argument naming and descriptions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2023 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-12 02:12:26 +00:00
depristo 6c9f86bb4d Removed unnecessary output and added debugging print() routine 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2020 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 18:37:36 +00:00
hanna 8406325247 New Picard is breaking one of the integration tests. 
Revert until we find out whether the cause is legit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2017 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 03:59:32 +00:00
hanna 499e7d1d75 Push forward some more delicate merging routines. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2016 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 03:07:34 +00:00
hanna bae4d3f7ea Updated Picard with fix for Doug Voet. Thanks Alec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2015 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-11 02:01:08 +00:00
hanna 2e4782f202 Command-line arguments for SamReadFilters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2014 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 23:36:17 +00:00
hanna 2cf9670d1e Allow users to directly specify filters from the command-line, applicable to 
any walker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2012 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 18:40:16 +00:00
ebanks 6a37090529 Output changes for VCF and UG: 
1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 16:31:31 +00:00
depristo d316cbad4c VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 13:24:58 +00:00
aaron f9819d5f13 a little clean-up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 06:18:34 +00:00
aaron 2ed423ed56 print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-10 05:57:01 +00:00
ebanks 2fa2ae43ec Enough people have found this useful, so... 
Moving Callset Concordance tool to core and adding integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:59:18 +00:00
ebanks 3793519bd4 -Added convenience method to VCF record to tell if it's a no call and have rodVCF use it before querying for info fields 
-Don't restrict info fields to 2-letter keys
[about to move these to core]


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2002 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 20:52:51 +00:00
ebanks 74751a8ed3 -Some minor fixes to get accurate vcf record merging done 
-Improvement to snp genotype concordance test

And with that, it looks like I get revision #2000.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2000 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 06:40:55 +00:00
ebanks 7ce0df76f8 Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:25:39 +00:00
ebanks d07f3bb6f6 Added methods to get strand bias and to test if record has allele freq or bias fields set. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-09 04:20:35 +00:00
kiran 3313b0ddb4 Fixed a minor bug where the lodThreshold wasn't being printed in the header. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:51:36 +00:00
kiran 567f5758d2 Optionally lists read depths by read group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 16:39:19 +00:00
hanna 21c5f543fa Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an 
alignment start will confuse the sharding system and cause it to return duplicate reads.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-08 14:27:26 +00:00
ebanks d549347f25 Refactored GenotypeLikelihoods to use an underlying 4-base model. 
It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 21:59:25 +00:00
aaron aacd72854f a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads. 
Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1).  Updated and checked BamToFastqIntegrationTest MD5 sums.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-05 05:26:33 +00:00
ebanks a545859c62 Joint Estimation model now emits a reasonable slod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 21:12:42 +00:00
ebanks 11d950abe0 No longer allow the lod_threshold argument - use confidence instead. 
Have UG output qscores in all cases.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:18:51 +00:00
asivache 2fb45dbd73 Make window size a command line argument 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:13:35 +00:00
asivache 55f61b1f88 Bug fix in adjustment of the shift position. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-03 16:08:11 +00:00
ebanks 3a33401822 2nd stage of the genotyper output refactoring is complete. 
Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 22:43:08 +00:00
aaron ba67c7f02b added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 21:09:18 +00:00
aaron b71b66bd88 the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-02 20:22:25 +00:00
ebanks af6d0003f8 -Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out). 
-Make rods return the appropriate type of Genotype calls from getGenotype().



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-01 05:35:47 +00:00
asivache 4b0796ba58 After fixing a few glitches and bugs, this version finally works as intended 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-31 04:59:58 +00:00
asivache ea8d5c7077 Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 17:50:51 +00:00
ebanks 4ee1d6f733 -Have the calculation models determine whether a call passes the lod/confidence thresholds (as opposed to returning everything and letting the UG decide); this way, walkers which call map() will get only the good calls. 
-Do the right thing in all models for all-base-mode (for Kiran).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-30 02:35:51 +00:00
asivache e3b4d4cbed Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1936 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 19:09:16 +00:00
ebanks 5cdbdd9e5b now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 13:27:37 +00:00
ebanks 3091443dc7 Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron. 
Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 03:46:41 +00:00
depristo 86573177d1 Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1929 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-29 01:04:37 +00:00
aaron 5a3bd50537 adding error log reporting to the GATK, and a stream based output method for the argument collection 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1926 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-28 19:56:05 +00:00
aaron 04e9a494e9 removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1924 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-28 18:08:14 +00:00
depristo 186a8dd698 Trivial protection for null value 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1918 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-27 21:52:52 +00:00
depristo 726378be8b Almost ready to stop doing eagar decoding; waiting on Eric 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1914 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-27 15:28:05 +00:00
aaron 3fb3773098 a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1912 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 20:18:55 +00:00
hanna a1e8a532ad Support for initialize() and onTraversalDone() output from parallelized walkers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-26 20:18:31 +00:00
ebanks 75ad6bbef7 Check that map isn't being called passing in null arguments. 
(This seems wrong; see JIRA entry GSA-211)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-25 02:30:36 +00:00
hanna 65b98470f3 Temporary fix: have RodLocusView manage and close its RODs. Really the 
relationship between these two classes needs to be rethought; see JIRA
GSA-207.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 16:00:12 +00:00
aaron 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. 
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
ebanks 6c338eccb8 Joint Estimation model now emits calls in all formats. 
The whole GenotypeCall framework needs to be changed, but this will work for the time being.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1902 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-23 03:07:28 +00:00
ebanks 54c61c663c -Cleanup of the Joint Estimation code 
-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 15:25:29 +00:00
asivache 2cab4c68d4 Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1898 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 14:55:07 +00:00
ebanks 55fa1cfa06 -Renamed new calculation model and worked out some significant xhanges with Mark 
-Allow walkers calling the UG to pass in their own argument collections


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1896 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 20:49:36 +00:00
ebanks 9b9744109c Mark's new unified calculation model is now officially implemented. 
Because it doesn't actually use EM, it's no longer a subclass of the EM model.

Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger).  I need to deal with general UG output tomorrow.  Hold off until then, Mark, and then you can go wild.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 02:39:23 +00:00
depristo caa3187af8 Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1890 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 23:31:13 +00:00
depristo 449a6ba75a Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 12:23:36 +00:00
ebanks b8ab77c91c Don't filter out reads without proper read groups. Instead, allow the user (or another walker calling UG) to specify an assumed sample to use (but then we assume single-sample mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1883 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 01:30:53 +00:00
ebanks c29924e7cf Reverting previous change. 
Aaron, it's all yours...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:55:24 +00:00
aaron d21b582b18 memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1880 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:39:42 +00:00
ebanks 761a730758 assertBiAllelic -> assertMultiAllelic. 
Chris, if this breaks an integration test, you get it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:09:46 +00:00
aaron cfa86d52c2 ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:00 +00:00
ebanks 51f9ec0a5c subtract largest posterior value from all values; this hopefully solves any precision issues 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1870 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:20:15 +00:00
ebanks b9e8867287 -push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures 
-use slightly more stringent stability metric
-better integration test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1869 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 04:22:17 +00:00
chartl ad777a9c14 @BasicPileup - made the counts public so they can be used 
@PoolUtils - split reads by indel/simple base

@BaseTransitionTable - complete refactoring, nicer now

@UnifiedArgumentCollection - added PoolSize as an argument

@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model

@GenotypeCalculationModel - instantiates with the new PoolSize argument




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1867 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 21:56:56 +00:00
andrewk d1a4cd2f73 Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval". 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:39:08 +00:00
ebanks 418e007ca6 A cleaner interface: now everyone can use UG's initialize method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1860 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 14:09:16 +00:00
aaron 96972c3a5c a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly. 
Also moved a buch of Lists over to Sets for consistancy.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:57:50 +00:00
aaron a69ea9b57c Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially. 
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:11:34 +00:00
ebanks 993c567bd8 I had to remove some of my more agressive optimizations, as they were causing us to get slightly different results as MSG. Results in only small cost to running time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1856 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 00:59:32 +00:00
asivache 7d7ff09f54 throw an exception if read has no associated read group 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 18:11:32 +00:00
depristo 0c2016c19a Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 12:07:44 +00:00
ebanks a32470cea1 Deal with the fact that walkers can call UG's init/map functions directly. 
We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 02:31:45 +00:00
ebanks e740e7a7ce Because walkers call UG's map function, we need to move the actual writing out 
to UG's reduce function.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1845 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:49:26 +00:00
ebanks 52d2e0ca07 All walkers now use read.getReadGroup() 
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
aaron eb90e5c4d7 changes to VCF output, and updated MD5's in the integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:42:48 +00:00
ebanks 89771fef05 -Use read.getReadGroup() 
-Add another filter for read groups for Chris


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1835 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:08:32 +00:00
ebanks 311ab8da5a A helper class to create the masks for the sequenom design maker. 
This project is now officially done.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1834 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:28:51 +00:00
ebanks 0c95d6906f Merge both versions of the Sequenom assay design maker: use Jared's base code and add in indels. [Jared, this still emits the same output for SNPs as your original version) 
Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:11:45 +00:00
ebanks f2886d88e0 We now emit genotype calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1828 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 02:49:56 +00:00
ebanks 96b8499a31 Remodeled version of the UnifiedGenotyper. 
We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases.  Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1821 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:27:01 +00:00
aaron 77499e35ac fixes for GSA-199: Need easier way to write binary outputs to standard output. GLF and VCF now have stream constructors, and can get dumped to standard out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1818 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 15:50:20 +00:00
ebanks caf689821f added method to get normalized posteriors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1809 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 02:33:22 +00:00
ebanks cf7a26759d -use the getReadGroup() function that was added to picard for us 
-clean up some include lines


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1808 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 01:39:32 +00:00
hanna d844d1c496 SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 19:16:46 +00:00
hanna da084357db Fixed minor typo in output message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1806 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 18:56:54 +00:00
ebanks a9f3d46fa8 Your time has come, SSG. 
Fare thee well.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1799 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 20:27:56 +00:00
aaron 98e3a0bf1a VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:50:04 +00:00
kiran 29ad6cd876 Made redundant by BCMMarkDupes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1795 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:47:20 +00:00
ebanks 15bf014e0b logger.info -> logger.debug (don't want to risk filling up my log on genome-wide calls) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1792 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 17:53:11 +00:00
ebanks 04fe50cadd *** We no longer have a separate model for the single-sample case. *** 
For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input.  For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.

The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you.  More on that in a separate email.
Other minor cleanups added too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 14:08:57 +00:00
kiran 829e99413b Rescores a variant after removing duplicates (defined very strictly as reads with the same start points). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1782 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 03:07:36 +00:00
ebanks 1905b5defa Hash by chromosome for now to reduce memory. This is a temporary solution until we decide how to reture the Injector for good. 
Also, with Picard's latest changes, we need to make sure we don't double-close the sam writer.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1779 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 20:06:25 +00:00
ebanks 203c626fc2 A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper. This wrapper incorporates both strand-based likelihoods and a combined likelihoods over both strands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1777 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-07 19:57:37 +00:00
depristo 8dd0924b37 Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1772 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 23:40:30 +00:00
aaron 4554ca1b28 more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 19:09:27 +00:00
aaron 3aec76136f Removing the AllelicVariant interface, which is replaced by the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 17:44:24 +00:00
aaron 66fc8ea444 GSA-182: Adding support for BED interval files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-06 02:45:31 +00:00
hanna aec83b401d SSG multithreading doesn't play well with some I/O changes made since I last svn up'd. Reverting until I can find the reason. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1766 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 19:48:57 +00:00
hanna 8a503c86b6 Code supporting SSG proof-of-concept shared memory parallelism. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1765 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 18:56:16 +00:00
ebanks fb619bd593 -Refactoring: make GenotypeCalculationModel constructors empty so that they don't have to be updated every time we add a new parameter; instead put that logic in the super class's initialize method (making everything protected so that only the factory can access them) 
-Adding initial version of Multi-sample calculation model.  This still needs much work: it needs to be cleaned up and finished.  Right now, it (purposely) throws a RuntimeException after completing the EM loop.

Also:
-Fix logic in GenotypeLikelihoods.setPriors
-Add logger to the models for output






git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1764 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-05 18:10:36 +00:00
aaron 7fc4472e6d A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). 
Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 19:35:35 +00:00
ebanks 53a4bd7f51 A better understanding of what's going on means no need for clearing the cache 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1755 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-02 18:07:46 +00:00
aaron e885cc4b21 changes for corrected GLF likelihood output, along with better tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1754 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-01 20:45:05 +00:00
aaron 2e4949c4d6 Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:37:59 +00:00
ebanks 303972aa4b Yup, I broke the build... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1750 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 20:20:43 +00:00
ebanks 841d25cc44 Added ability to set the priors after construction (and requiring a flushing of the likelihoods cache) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1749 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-30 19:55:49 +00:00
hanna 70e1aef550 Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 22:23:19 +00:00
aaron b1c321f161 Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 21:28:21 +00:00
ebanks 9ef80e3c3c One minor addition: to incorporate Pooled calling (and to be as general as possible), we allow the genotype calculation model to use rods if it wants. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1741 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 17:05:59 +00:00
ebanks 19bfe43173 First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class. 
Some notes:
1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris.
2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878.  Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts.
3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 16:48:15 +00:00
andrewk 5dab95aa5a Fix getMergedReadGroupsByReaders so that it provides read groups in the same way Picard does so that it works correctly when input read files have no clashes in their read groups and retain their original read group names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1737 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-29 06:35:50 +00:00
asivache bce2f0d7cf Now instantiates the list of alternative consenses to evaluate as LinkedHashSet to guarantee iterator traversal order. Old implementation used HashSet and exhibited unstable behavior when two alt consenses turned out to be equally good: depending on the run conditions (including size of the interval set being cleaned??), either one could be seen first as selected as the 'best' one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1734 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-28 06:15:46 +00:00
asivache 663175e868 Bug fix: when jumping onto next contig (chromosome), the walker was erasing last mismatch interval from the previous chr it was still holding without printing it; now it gets printed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1733 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 22:24:34 +00:00
asivache aec61c558b moving IndelGenotyper out from playground 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1731 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 19:43:53 +00:00
aaron 2b7d39035a switched over the FastaAlternateReferenceWalker to the Variation system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1726 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 16:09:43 +00:00
aaron 7ffc1d97ef Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1724 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-25 04:35:52 +00:00
aaron d2af26e81f Pooled EM SNP Rod converted over to the Variation interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1719 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:33:11 +00:00
ebanks 97105ac001 We need to return a null RODRecordList when the default value is null (as opposed to a list with a single null value), because that's what everyone is expecting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1718 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:23:12 +00:00
ebanks d4b40bc06f Filter for reads with missing read groups so we can safely assume all reads have valid read groups 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1717 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 16:10:26 +00:00
ebanks 90de2e0cde Added ability to specify whether you want to use a point estimate or fair coin test calculation; for now you can use either but fair coin test is still experimental as it needs to be parametrized correctly. This job will hopefully be done by the future Bioinformatic Analyst... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1716 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 15:29:50 +00:00
aaron d262cbd41c changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-24 15:16:11 +00:00
ebanks 423a3ee894 Added a sequenom rod to empower Carrie to convert 1KG validation SNPs to sequenom format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1706 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 20:22:09 +00:00
hanna 856bbd0320 Let Picard specify the default compression level. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1701 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 19:01:48 +00:00
aaron f783cb30e0 adding an interface so that the current @Requires with ROD annotations work in walkers like VariantEval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1700 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:24:05 +00:00
hanna ebfbe56b43 Make sure compression level always gets pushed into SAMFileWriterFactory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1699 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:20:26 +00:00
asivache bf7cd66d53 New, simpler rodRefSeq. Fully relies on the ROD system standard mechanisms. Multiple transcripts over a given location will be now returned by the ROD system itself as RodRecordList<rodRefSeq>; and yes, rodRefSeq does represent a single transcript record now and implements Transcript interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1697 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:18:25 +00:00
asivache 8fa4c93f5a Transcript is now simply an interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1696 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:13:31 +00:00
asivache 1bd4c0077c Now that ROD system supports overlapping RODs, we do not need rodRefSeq to be too smart and read in all the overlapping records (transcripts) on its own; leave it to the generic ROD mechanism. 
PARTIAL commit; new, simpler rodRefSeq will reappear in a seq.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1694 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-23 18:11:16 +00:00
aaron 11c32b588f fixing VariantEvalWalkerIntegrationTest md5 sums, a couple comment changes, and a little bit of cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1690 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:54:47 +00:00
ebanks 0748d80baa Added a convenience method in rodDbSNP to deal with Andrey's changes to the rod. Now you can just ask for the first real SNP rod from the list and not have to think about how it works. 
CountCovariates uses it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1688 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 20:15:40 +00:00
ebanks 682b765536 bug: need to upper case chars so that == works throughout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1684 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 18:20:43 +00:00
asivache 57d31b8e9b Filter that discards reads from specific lanes; and also its friend that helps blacklisting a set of lanes from GATK command line a one-liner. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1681 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 16:46:06 +00:00
ebanks 5ce42cbab3 After thinking about this a bit more, it makes sense to pull this functionality out of my walker and into the GenomeLocParser where everyone else can benefit from it... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1677 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-22 01:32:35 +00:00
ebanks b1dc6d65e4 interval merging is now blazingly fast 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1674 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 21:15:04 +00:00
asivache 15135788ca OK, let's bite the bullet. Now rodDbSNP objects are 'isSNP()' only when they are annotated as 'exact', not a 'range'. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1673 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 19:25:16 +00:00
asivache 8ad181f46f Note to myself: do 'ant clean' now and then or old versions of the code that suddenly became invalid will stick around. The world is not perfect, and neither is automatic dependency resolution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1672 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:40:52 +00:00
asivache d2d1354199 Now uses BrokenRODSimulator class to pass the test. CHANGE the code to use new ROD system directly and MODIFY MD5 in corresponding tests, since a few snps are seen differently now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1670 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 17:03:49 +00:00
asivache 29adc0ca1c Little class that can be used to simulate the results returned by the old ROD system. This is needed to keep couple of tests from breaking. All the code that uses this class must be changed urgently to accomodate the data as returned by new ROD system, and the corresponding tests (MD5 sums) have to be modified as well since some data as seen through the new ROD system is indeed different. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1668 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:58:56 +00:00
asivache a6bd509593 Changing the carpet under your feet!! New incremental update to th eROD system has arrived. 
all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1667 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:55:22 +00:00
asivache 4c67a49ccb Removed unused imports 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1666 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 16:45:22 +00:00
hanna e7f44ada98 Make unpackList public static so that Doug can use it in the scatter/gather framework. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1665 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 15:32:49 +00:00
ebanks 7b627fd622 Check for empty interval lists to merge 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1664 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-21 04:34:26 +00:00
hanna 7f5778c966 Update gsadevelopers -> gsahelp. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1663 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-20 23:36:54 +00:00
aaron 3a487dd64e little fixes; also fixed a tyPo 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1662 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 22:38:51 +00:00
aaron b6d7d6acc6 fix for the eval tests, and a change to the backedbygenotypes interface, more changes to come 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1661 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 22:25:16 +00:00
depristo 4318f75910 tiny cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1660 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 21:04:25 +00:00
depristo 3a341b2f06 Fixes for VariantEval for genotyping mode 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1659 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 21:01:43 +00:00
aaron 7b39aa4966 Adding the VCF ROD. Also changed the VCF objects to much more user friendly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1658 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 20:19:34 +00:00
ebanks b19fd4d45c Damn unit tests have a null Toolkit()... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1654 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 17:10:49 +00:00
ebanks 90626c843d oops - we don't need reference bases, but we still need reference 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1653 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 16:24:45 +00:00
ebanks 2b2df4e1ba - Fix the CleanedReadInjector to deal with -L intervals correctly. 
- Some walkers don't use the ref base, so speed up traversals by not requiring it


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1652 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 16:17:58 +00:00
asivache 94618044e8 Starting an update of ROD system. These basic classes will completely replace old ones, but with this update they are not linked to anything, so this checkpoint should be safe. 
The main reason for the change is that there can be (and are!) multiple RODs overlapping with a single reference base position in a single track. There can be two "trivial" RODs at the same location (e.g. samtools pileup will have two point-like records at putative indel sites: one for the reference, the other one for the indel itself). Or there can be one or more "extended" RODs (length >1), eg. dbSNP can report an indel at Z:510-525 AND a SNP at Z:515.

The ReferenceOrderedDatum object (and children) will not be changed, but it is now explicitly interpreted as a single data *record*, possibly out of many available from a given track for the current site. As long as single data record occupies one line in a data file, the new ROD system will take care of loading and keeping multiple records, including extended (length > 1) ones, and will automatically drop the records when they finally go out of scope. For one-line-per-record, multiple-records-per-site RODs, there is no need anymore for the hack used so far that involved passing ROD's own implementation of iterator through reflection mechanism (though it will still work)

* RODRecordList: 
the ROD system (its iterators) will now always return a LIST of all RODs available at current position or at current query interval (see below). This class is a trivial wrapper for a list of ROD objects, with added location argument for the whole collection. The location of the RODRecordList is where the ROD system is currently sitting at: a single, current base on the reference (if next() traversal is performed), or the location of the query interval when returned by seekForward() (see below). The ROD objects themselves will have their locations set according to the original data in the file. Hence, perusing the above example of a dbSNP indel at Z:510-525 and SNP at Z:515, when moving to the position Z:515 the ROD system will return a RODRecorList with location Z:515, and with two ROD objects packaged inside, one with location Z:510-525, the other with Z:515.

*RODRecodIterator:
Almost identical to old SimpleRODIterator used by ReferenceOrderedData; this is a low-level iterator that walks over records in the data file (with a callback to ROD's ::parseLine() to parse real data)

*SeekableRODIterator:
a decorator class that wraps around Iterator<ROD> (such as RODRecordIterator) and makes the data traversable by reference position, rather than record by record. This is reimplementation of the old RODIterator.  SeekableRODIterator's ::next() moves to the next position on the ref and returns all RODs overlapping with that position (as a RODRecordList). This iterator also adds a seekForward(loc) operation, that allows fast forwarding to a specified position or interval. Length > 1 query arguments (extended intervals) are fully supported by seekForward(), the returned RODRecordList wil contain all RODs overlapping with the specified interval, and the location of the returned RODRecordList object will be set to that query interval. NOTE: it is ILLEGAL to perform next() after a seekForward() query with length > 1 interval. seekForward() with point-like (length=1) interval reenables next().


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1650 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-18 15:58:37 +00:00
hanna 355136928e Play nice with other jobs in this VM -- don't close stdout / stderr. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1646 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-17 18:55:08 +00:00
ebanks 5d85bd9671 By default, VF should ask for deleted bases so that they show up in coverage. 
The Strand filter then needs to ignore those bases when determining bias.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1636 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 16:46:09 +00:00
hanna 01a9b1c63b Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 08:33:56 +00:00
hanna 9f7cf73411 Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem. 
Sigh.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1630 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 21:06:45 +00:00
hanna 17758b381c Properly initialize redirected output streams in case of out and err. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1629 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 19:47:43 +00:00
andrewk 00dfe014b7 Added option to FastaReferenceWalker to change output FASTA file format's line width and to remove header lines; allows dumping raw sequence using intervals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1628 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 18:00:30 +00:00
hanna b69eb208a6 Always create output files, even if no output was written to them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1627 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 17:58:14 +00:00
aaron b401929e41 incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-15 04:48:42 +00:00
ebanks 01e7b39c8d 1. Don't print out values in filter field of the VCF. 
2. Fix ratio printouts (for params file)
3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1616 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 21:03:39 +00:00
ebanks 436f543b3b I owe Doug a beer for finding this: 
don't print out intervals to be merged if they're not within the global -L intervals


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1615 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 20:22:30 +00:00
aaron e03fccb223 Changes to switch Variant Eval over to the new Variation system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-14 05:34:33 +00:00
aaron 5b41ef5f70 rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1609 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-13 23:48:58 +00:00
ebanks c669e8d5ad Use constant seed in the random generator so we can be stable (and thus unit tests will work) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1607 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-13 17:40:56 +00:00
depristo 6c7a300664 Missing file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1601 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:17:09 +00:00
depristo 6e13a36059 Framework for ROD walkers -- totally experiment and not working right now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:13:15 +00:00
depristo e8d544869d Alignment context now supports the idea of skipped bases -- not currently in use 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1598 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:11:38 +00:00
depristo 3949b4ac72 commented out version of next() and hasNext() that appear to be correct but are causing testing problems 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1596 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:09:21 +00:00
depristo 58105636c8 getBoundRods() convenience method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:07:57 +00:00
depristo 4e1eded389 Fixed bad compareTo operator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1594 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:07:10 +00:00
depristo 7c8b17b456 fix for SSG with pl name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1591 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-11 20:39:34 +00:00
chartl d6a0b65ac9 Changes: 
Rollback of Variant-related changes of r1585, additional PGC code




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-11 16:23:01 +00:00
chartl 0c54aba92a Changes: 
@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.

@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.

@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.

Added:

@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
 and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-11 15:01:50 +00:00
aaron 5a64a80ab5 changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 04:31:33 +00:00
depristo c988205884 Notes for Aaron in SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1576 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 03:18:51 +00:00
ebanks 1362a56227 Added fasta tests and small fix to cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 03:13:11 +00:00
depristo 0093482c62 N reference base fix for SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1572 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 21:19:36 +00:00
ebanks cb31d5a0ab VariantFiltration now outputs VCF. Important changes: 
1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD.
2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF.
If there are any problems, go find Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1569 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 20:04:32 +00:00
asivache dd0085c428 1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call) 
2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N'
3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 20:04:04 +00:00
ebanks 542af6402e output correct format for Sequenom SNPs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1567 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 19:21:53 +00:00
kiran 3b1e966b4c Lowercases the sequencing platform so that a difference in case doesn't lead to the failure to look up an entry in the hash. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1565 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 17:35:45 +00:00
kiran d82d6c0665 Excludes variants that fall below a certain LOD that changes as a function of depth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1564 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 17:34:16 +00:00
kiran 06eae52292 Throws an exception if you attempt to use a filter that doesn't exist. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1563 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 17:33:27 +00:00
asivache 1060b36288 Bug fix: 'N' cigar elements now treated properly; for all practical intents and purposes, N is the same as D and should be treated as such, the difference is only in logical interpretation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1562 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 17:08:35 +00:00
chartl 9d69bd2c84 Modifications: 
@CoverageAndPowerWalker - removed a hanging colon that was being printed after the reference position

@VariantEvalWalker - added a command line argument for pool size for eventual use in doing pooled caller evaluations. As now, the variable is unused.

@AlignmentContext - altered the scope of class variables from private to protected in order that child objects might have access to them


New Additions:

Filtered Contexts

Sometimes we want to filter or partition reads by some aspect (quality score, read direction, current base, whatever) and use only those reads as
part of the alignment context. Prior to this I've been doing the split externally and creating a new AlignmentContext object. This new approach makes
it a bit easier, as each of these objects are children of AlignmentContext, and can be instantiated from a "raw" AlignmentContext.

@FilteredAlignmentContext is an abstract class that defines the behavior. The abstract method 'filter' is called on the input AlignmentContext, filtering
those reads and offsets by whatever you can think of. The filtered reads/offsets are then maintained in the reads and offsets fields. These classes can
be passed around as AlignmentContexts themselves. Writing a new kind of read-filtered alignment context boils down to implementing the filter method.

@ReverseReadsContext - a FilteredAlignmentContext that takes only reads in the reverse direction

@ForwardReadsContext - a FilteredAlignmentContext that takes only reads in the forward direction

@QualityScoreThresholdContext - a FilteredAlignmentContext that takes only reads above a given quality score threshold (defaults to 22 if none provided).

A unit test bamfile and associated unit tests for these are in the works.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1559 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:49:52 +00:00
depristo d9588e6083 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 
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
asivache df11618092 Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1556 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:09:09 +00:00
depristo eeb9b6eb13 GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 10:39:14 +00:00
ebanks 0cc219c0df -Added unit test for walkers dealing with intervals for cleaning 
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been.  Hooray for unit tests!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 02:35:17 +00:00
depristo ec0f6f23c7 LocusIterationByState is now the system deafult. Fixed Aaron's build problem 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 01:28:05 +00:00
ebanks 5dbba6711c Lots of changes: (I'll send email out in a sec) 
1) Moved various disparate concordance / set splitting functionalities to a new parent tool which works like VariantFiltration (i.e. people can write various modules that fit inside and can be run though it).
2) Fixed up argument parsing in VariantFiltration to use key=value format so we don't accidentally mox up values (like I had been doing).
3) Have indel rod print samples


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1540 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-07 01:12:09 +00:00
depristo 1c3d67f0f3 Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 22:26:57 +00:00
depristo 2b0d1c52b2 General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 19:13:37 +00:00
aaron 0cc634ed5d -Renamed rodVariants to RodGeliText 
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 18:40:43 +00:00
ebanks fd1c72c151 Fixed package name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1535 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 15:40:06 +00:00
ebanks 6c476514f8 Moved to core. Wiki pages are going up; unit tests will be written soon. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1533 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 15:09:11 +00:00
ebanks 849dce799d This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1531 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 14:21:46 +00:00
depristo a08c68362e Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 12:39:06 +00:00
aaron 3c2ae55859 changes for the genotype overhaul. Lots of changes focusing on the output side, from single sample genotyper to the output file formats like GLF and geli. Of note the genotype formats are still emitting posteriors as likelihoods; this is the way we've been doing it but it may change soon. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1529 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 05:31:15 +00:00
ebanks 5bd99fc1c4 VariantFiltration moved to core. 
Another win for the team.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1517 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-03 15:41:41 +00:00
depristo bdd0a6f9fa change to make build work 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-03 13:43:10 +00:00
depristo b01ac9de0c High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1510 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-03 03:06:25 +00:00
ebanks 3dfc77dc89 Add an indel rod which represents the initial point of the indel only 
(useful for alternate reference making)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-02 19:32:29 +00:00
aaron 0e6feff8f2 fixed locus pile-up limiting problem 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1505 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-02 16:56:44 +00:00
aaron 05c164ec69 changing the default behavior to allow any sized read pile-up (which may exceed the memory limit); the user can then select their own read limit. The default of 100K was arbitrary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1498 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 14:46:00 +00:00
ebanks 54c0b6c430 Allow this ROD to consist of just the positions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1497 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 12:43:18 +00:00
aaron 4a1d79cd7b added a flag, maximum_reads_at_locus, shortName "mrl", which limits the number of reads we add to the locusByHanger. In some bam files misalignment produces pile-ups of 750K or more reads. We now limit this to the default of 100K reads. 
The user is warned if a locus exceeds this threshold, and no more reads are added.

Also CombineDup walker had an incorrect package name.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1496 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 04:21:58 +00:00
ebanks 0addae967a IndelArtifact filter can now handle filtering false SNPs that occur within the span of an indel but after the first position 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1495 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-01 03:34:39 +00:00
ebanks 8e3c3324fa Added filter for SNPs cleaned out by the realigner. 
It uses the realigner output for filtering; in addition, dbsnp indels partially work; IndelGenotyper calls don't yet work.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1489 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 04:32:32 +00:00
ebanks 8bc7afe781 Smarter SW penalties 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1488 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 04:29:19 +00:00
ebanks 1a299dd459 Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1486 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 03:31:37 +00:00
ebanks 215e908a11 Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters. 
This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-31 02:16:39 +00:00
depristo 813a4e838f Removing old code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1482 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 19:27:11 +00:00
depristo 49a7babb2c Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 19:16:30 +00:00
depristo 522e4a77ae Caching support across multiple technologies 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1480 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 18:10:14 +00:00
depristo 5af4bb628b Intermediate checking before code reorganization. Full blown support for empirical transition probs in SSG for all platforms. Support for defaultPlatform arg in SSG. Renaming classes for final cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1479 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 17:34:43 +00:00
depristo bde67428fd Better formatting of the code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1477 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-29 21:46:47 +00:00
aaron 8331c195fb changed the full name of maximum_reads to maximum_iterations for consistancy 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1475 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 16:03:46 +00:00
depristo 8e129d76fd Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 14:14:21 +00:00
depristo bf60980653 Experitmental support for empirical P(B_true | B_miscall). --useEmpiricalTransitions flag to SSG enables this support. Much better implementation of Genotype likelihoods -- the system should scream along now. Continuing progress towards deleting old model 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1469 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 00:17:24 +00:00
depristo 7cf9a54b64 change for new char/byte in BaseUtils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1467 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-27 23:47:56 +00:00
hanna e5115409fa Force columnSpacing to be at least one. We need a general-purpose, working tool for outputting columnar data to a PrintStream; will add JIRA. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1457 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-25 19:54:54 +00:00
hanna ccdb4a0313 General-purpose management of output streams. 
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
aaron cd711d7697 Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric. 
also fixed some verbage in the GAEngine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1449 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-21 05:35:49 +00:00
aaron 6313c465fb we want the RMS of the reads qualities not the RMS of the RMS of the read qualities. 
Also the VCF version tag seems to be standardized as VCR.  Updated the VCF code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1447 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-20 21:56:29 +00:00
ebanks ed8c92a12a make isReference do the right thing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-19 20:32:29 +00:00
ebanks b3fe566c0c Fix descriptions of walker args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1436 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-18 19:46:48 +00:00
ebanks 53153fcd79 Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1433 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-18 15:26:10 +00:00
ebanks b2a18a9d61 - first pass at a basic indel filter (for now, based on size and homopolymer runs) 
- fix simple indel rod printout


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-18 03:04:12 +00:00
jmaguire 1e8b97b560 quietly skip empty intervals files rather than crash. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1428 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-17 20:19:14 +00:00
jmaguire 92c63fb530 It's just "lod" not discovery_lod now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1427 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-17 18:44:09 +00:00
ebanks df5744bcd3 update this walker so any variants can be passed in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1426 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-17 16:30:39 +00:00
aaron d101c20b30 added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 22:10:20 +00:00
ebanks 2c3f56cb8d fix length calculation (it was including +/- char when it shouldn't) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1410 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 20:28:24 +00:00
aaron fc1c76f1d2 fixing a bug where reads in overlapping interval based locus traversals could get assigned to only one of two the regions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1407 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 17:50:16 +00:00
ebanks ecae619a1b warn user when dbSNP rod looks suspicious 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1400 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:20:20 +00:00
asivache 2841e151d0 javadoc comments only 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 18:44:35 +00:00
ebanks 02f1af0743 Don't die when a readgroup is absent from the covariates table - it could 
happen when all reads are unmapped (or have MQ0); instead, just don't alter
the quals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1394 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 03:10:33 +00:00
depristo 6d3ef73868 Now includes statistics on the allele agreement with dbSNP -- counts concordant calls as dbSNP = A/C and we say A/C, vs. we say A/T 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1392 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:37:07 +00:00
depristo 20baa80751 Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1391 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:01:04 +00:00
depristo bbd7bec5db Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 22:25:30 +00:00
hanna 48713e154c Windowed access to the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 16:29:15 +00:00
depristo 65e9dcf5b7 Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 01:00:55 +00:00
depristo 4dc23f2763 Trivial formatting changes as I moved more legacy code into this system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1381 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 00:54:26 +00:00
depristo 34af669dbb Explicit ENUM representation of the diploid genotypes. Please use this from now on to represent strings like AA or AT 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1380 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 00:53:43 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
depristo 20ff603339 New hotness and old and Busted genotype likelihood objects are now in the code base as I work towards a bug-free SSG along with a cleaner interface to the genotype likelihood object 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1372 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 23:07:53 +00:00
depristo 4986b2abd6 Fixing bug in SSG -- genotyping and discovery were mixed up by name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1371 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 22:13:35 +00:00
depristo 3485397483 Reorganization of the genotyping system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1370 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 20:55:31 +00:00
depristo d840a47b11 Slight reorganization of genotype interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-03 19:17:15 +00:00
ebanks 4366ce16e0 Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 14:53:27 +00:00
ebanks feb7238f10 Wasn't always returning the correct alt base 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-30 03:08:04 +00:00
hanna 5429b4d4a8 A bit of reorganization to help with more flexible output streams. Pushed construction of data 
sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.  


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 23:00:15 +00:00
hanna 7a13647c35 Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 16:11:45 +00:00
ebanks 3c4410f104 -add basic indel metrics to variant eval 
-variants need a length method (can't assume it's a SNP)!


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-28 03:25:03 +00:00
aaron f1109e9070 Added the interator to SAMDataSource to prevent seeing dupplicate reads, only in a byReads traversal. The iterator discards any reads in the current interval that would have been seen in the previous interval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1317 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-25 22:36:29 +00:00
asivache a361e7b342 SAMDataSource is now exposed by GATK engine; SamFileHeaderMerger is exposed from Resources all the way up to SAMDataSource, so now we can see underlying individual readers should we need them; GATK engine has new methods getSamplesByReaders(), getLibrariesByReaders(), and getMergedReadGroupsByReaders(): each of these methods returns a list of sets, with each element (set) holding, respectively, samples, libraries, or (merged) read groups coming from an individual input bam file (so now when using multiple -I options we can still find out which of the input bams each read comes from) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1315 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 22:59:49 +00:00
hanna 2024fb3e32 Better division of responsibilities between sources and type descriptors. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1314 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 22:15:57 +00:00
ebanks 59f0c00d77 -set indel cleaning walkers to be in core package 
-move Andrey's alignment utility classes to core


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 05:23:29 +00:00
aaron 0b16253db3 an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 23:59:48 +00:00
ebanks 477502338f moved major indel cleaning pieces to core (yippee!) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1301 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 19:59:51 +00:00
ebanks 4efe26c59a Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found. 
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
ebanks ee8ed534e0 print full genotype for alt allele 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 01:35:23 +00:00
depristo 9c12c02768 AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-22 17:54:44 +00:00
hanna 6e4fd8db4a Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1290 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 22:23:28 +00:00
depristo 761d70faa1 Better printing of multiple rods -- now produces a comma-separated set of values 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 21:58:27 +00:00
depristo 8588f75eb6 Better printing with toSimpleString() -- now prints out chip-genotype string 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1288 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 21:57:59 +00:00
hanna 1843684cd2 Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 18:50:51 +00:00
hanna b43925c01e Switched to Reflections (http://code.google.com/p/reflections/) project for 
inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 18:32:22 +00:00
kiran 436a196e2b Bug fixes to support hapmap genotyping concordance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1285 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 16:20:10 +00:00
aaron f13a1e8591 adding a couple of small changes to support contract with VariantEval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1283 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 03:49:15 +00:00
aaron b4adb5133a GLF rod as a AllelicVariant object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 00:55:52 +00:00
ebanks 54fce98056 duh, don't print newline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1280 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-20 03:04:27 +00:00
ebanks 1d2b545608 add FLT toString method (to be used in PrintRODs) and add it to ROD list 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-20 02:47:50 +00:00
ebanks 387316ebe1 added indel rod 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1276 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 16:05:51 +00:00
ebanks da4af3b620 print indels in the format required for 1KG submissions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 15:59:18 +00:00
ebanks d45c90b166 ROD to represent simple output from IndelGenotyper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-17 14:36:12 +00:00
hanna df1c61e049 Re-add the plugin path. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1271 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 22:48:44 +00:00
hanna 7c30c30d26 Cleaned up some duplicate code in preparation for making plugin dir configurable. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1270 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 22:02:21 +00:00
depristo 107f42a01e Hacks for getting GLFs support in the Rod system working 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1268 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 21:03:47 +00:00
ebanks 88ffb08af4 Need to return real values for some of the AllelicVariant methods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1264 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-16 02:31:10 +00:00
ebanks ba349e8d52 add FLT ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1257 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 19:40:50 +00:00
ebanks 800f7e6360 make AllelicVariant extend ReferenceOrderedDatum (not Comparable) since ROD itself is Comparable. Then we can generalize RMD tags. 
Blame Matt if this doesn't work - he said it wouldn't break anything.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1256 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 19:25:06 +00:00
ebanks 5be5e1d45f added conversion from iupac format and new rod to deal with FLT file format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 18:34:41 +00:00
aaron d36e232ed3 adding GLF rods to the module list 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1252 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:42:34 +00:00
aaron 9ecb3e0015 adding GLFRods with tests and some other code changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:30:19 +00:00
hanna c25f84a01c Regression: we lost our hack to work around BAM files with index problems (affects BAM files created before 23 Apr 2009 and traversed by interval). Added the hack back in, along with a much more explicit comment about why its there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1248 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 14:41:37 +00:00
ebanks 513d43b5f3 now implements AllelicVariant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1246 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 14:06:25 +00:00
ebanks d369136bda depricate this ROD yet again 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1245 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 13:33:03 +00:00
ebanks efcbb16688 un-deprecate this ROD and make it implement Genotype 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1240 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 19:45:41 +00:00
depristo 84d407ff3f Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 18:53:27 +00:00
hanna 76b09a879b Display a more intelligent error message if the user runs a locus traversal across an unmapped reads file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1238 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 18:36:09 +00:00
hanna 99f9cd84ed Warning for possibly mismatched reads / reference was very aggressive. Relax 
the criteria a bit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1234 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 16:21:22 +00:00
hanna 12b5d9c70c The number of loci can easily overflow an int. Change reduce type to a Long. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1233 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 16:07:00 +00:00
depristo 5bf7647498 0.2.3 -- now preserves Q0 bases throughout the reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1232 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 12:27:31 +00:00
hanna 0f6bfaaf73 Skip validation in case of no reads aligning. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1230 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 02:03:36 +00:00
hanna bfe90af5e2 Some quick and dirty fixes to support querying unmapped BAM files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1228 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-14 01:25:20 +00:00
hanna 9f0fb9f3aa Fix for GSA-90: GATK banner and error messages should point to the wiki website. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1226 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-13 21:56:41 +00:00
hanna b18caa2052 Fix for GSA-90: System isn't failing with an error when you use the wrong reference. 
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
hanna 5c321f9630 Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1223 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-13 16:41:55 +00:00
ebanks 0070b8ea6a Until 454 goes far, far away, at least we can completely ignore it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1219 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-10 18:31:53 +00:00
asivache b08b121756 synchronyzing; debug statements commented out, so nothing changed really 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1215 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-10 16:38:33 +00:00
asivache a1eb128377 few more detailed debug printouts conditioned on if (DEBUG), so no real changes... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1214 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-10 16:36:57 +00:00
hanna 03e1713988 Better support for specifying read filters to apply directly from the walkers. 
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
aaron ce08f5f0c3 Removed some unused variables, fixed some javadoc. The usual. 
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
aaron 9cfd89c54f a small refactoring, and some documentation cleanup 
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
aaron d86717db93 Refactoring of the traversal engine base class, I removed a lot of old code. 
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
ebanks 3519323156 Output the correct geli text format 
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
ebanks 99631cdaa1 fix and then deprecate the rodGELI class (GELIs suck) 
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
hanna 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). 
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
ebanks 3fe7104963 Added walker to filter out clustered SNPs from a call set 
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
hanna 3f0304de5a Get rid of unused iterator. 
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
hanna da4d26b1ea Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing. 
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
ebanks aacec3aeb0 rod for binary GELI files (still needs to be tested) 
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
hanna 433ad1f060 Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application. 
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
hanna d8fbb2b62c Refactoring; make a better home for the MalformedReadFilteringIterator. 
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
hanna 4ba2194b5e Filter reads whose alignment starts past the end of the contig to which it allegedly aligns. 
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
hanna 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. 
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
hanna 5735c87581 Basic infrastructure for filtering malformed reads. 
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
hanna 31313481f6 Temporary patch to filter out bad alignments that aren't quite fully reported as bad. 
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
hanna d19366eaad Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes. 
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
jmaguire 4019cd2bd7 Added ROD for parsing hapmap3 genotype files. 
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
ebanks e5e249d4ac temporary fix to deal with screwy SOLiD reads 
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
depristo 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 
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
depristo bcda66d2db Simple performance improvements 
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
hanna 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. 
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
hanna 62807139fc Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 14:54:01 +00:00
aaron 1c83b4d949 forgot to take out some test code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 14:18:37 +00:00
aaron bc17ff567a When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 14:15:50 +00:00
depristo 47cb9f169e Stable tool that's the reverse of merging -- splits a file into individual BAM files, one for each sample ID in the SAM header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1155 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 12:56:46 +00:00
aaron bb92eb8b1c added a fix for overlapping reads in the locus context 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1153 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 02:08:59 +00:00
hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given 
the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 18:23:35 +00:00
aaron d58eeb7539 Don't cry wolf: only one warning is now emitted, instead of tons of warnings. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1139 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 13:50:37 +00:00
hanna a3e0ec20c4 Kill the TraverseByLocusWindows traversal. TraverseLocusWindows will take its place. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1138 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 13:46:35 +00:00
hanna e93f751bd7 First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-30 21:59:54 +00:00
aaron f5cba5a6bb Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-30 19:17:24 +00:00
depristo 9fca79ed62 Read groups are now sorted in the output data, for convenience 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-30 16:50:44 +00:00
aaron 03f8177a53 When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 20:51:55 +00:00
depristo 7ecc43e9a7 Fixed subtle null ptr exception discovered by Kiran. Now deals with the rare situation where you have only say Q28 bases at dbSNP sites, so you fail in the Table recalibration step with a null pointer error into the data structure indexed by quality score. If you are Q score above those seen before you aren't modified in any way. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1118 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 18:57:42 +00:00
ebanks 95e2ae0171 Deal with reads whose ends are aligned off the end of a chromosome. 
Includes update to ignore non-ATCG bases (not just 'N')
(Also, create a BWA dir for future work)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1117 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 16:50:05 +00:00
jmaguire 65a788f18a Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls. 
Some doodling around with indel calling in an EM context.
 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 16:32:12 +00:00
aaron d7d4298917 Some files to support generic genotype outputing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-26 15:43:41 +00:00
hanna 491ed70b44 TraverseByLocusWindow -- asstd bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:51:38 +00:00
depristo 5289230eb8 Version 0.2.1 (released) of the TableRecalibrator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:50:55 +00:00
hanna ad3a3aa350 First pass at passing lists of files / lists of interval arguments work. Note that the interval 
ROD system will throw up its hands and not deal with intervals at all if multiple interval files 
are passed in (see JIRA GSA-95). 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 20:44:23 +00:00
ebanks 83816fb801 Stop using the annoying refIterator (temp change until new traversal is green lighted) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1103 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 20:05:39 +00:00
ebanks 0d9041380d remove printouts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 18:54:14 +00:00
hanna 102b38c055 Sketch of new version of TraverseByLocusWindow, and a flag to conditionally turn it on. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1097 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 18:20:56 +00:00
aaron 5b1c23a7f2 changes to fix and test the interval based traversals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 17:54:15 +00:00
ebanks 347608cfe0 remove hacked traversal in preparation for move to Matt's new one 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 14:32:05 +00:00
depristo 0a50f2e160 Updated and near final version of tabular recalibration system. Uses 'yates' correction for low-occupancy quality bins. Faster and more robust handling of input and output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-24 03:52:12 +00:00
hanna ef546868bf Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude. 
Desperately needs cleanup.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-23 23:48:06 +00:00
aaron 8b4d0412ca Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-22 21:11:18 +00:00
aaron bcb64d92e9 Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-22 14:39:41 +00:00
depristo 26eb362f52 Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-21 21:27:40 +00:00
depristo d3f0c51944 longer update times so we don't overwhelm when running genome-wide 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1067 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-21 14:10:02 +00:00
depristo 9e26550b0d Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-20 16:00:23 +00:00
hanna dde52e33eb Cleanup of the cleaned read injector based on Eric's feedback. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-19 22:04:47 +00:00
depristo 8ac40e8e2d Updated version of the recalibration tool 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-19 17:45:47 +00:00
depristo d748c85dc4 Cleaned code and reorganized -- moving in the right direction for v2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-18 22:28:34 +00:00
depristo 1bca144119 Moving things around 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-18 21:06:46 +00:00
depristo 3c40db260d Added REFERENCE_BASES required annotation for performance 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-18 21:03:57 +00:00
kiran 7a921c908c Can now adjust the genotype likelihoods of a variant returned from the rod. This automatically causes the lodBtr, lodBtnb, and genotype to be recomputed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1041 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-18 07:26:37 +00:00
kiran c4d9058f32 Added module rodVariants.class to the list of allowable RODs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1037 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-17 21:33:13 +00:00
kiran ab2a80f3ea A new ROD type that allows one to input a geli.calls file back into a walker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1036 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-17 21:32:21 +00:00
hanna cba9025983 More package-level documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1030 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-17 16:28:45 +00:00
hanna 43a28750e0 Package level documentation -- helps new users get acclimated to the codebase more quickly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-17 16:27:48 +00:00
aaron 6ee64c7e43 added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 22:15:56 +00:00
aaron 7db4497013 fixing the readTraversal output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1019 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 19:44:38 +00:00
ebanks 647b8a1ab0 Fix TabularROD printing and testing so Aaron stops nagging me. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 15:49:26 +00:00
aaron a0a549557f added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file. 
Also fixed a bunch of documentation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1015 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-15 22:15:03 +00:00
ebanks 11aa715630 added capability for filtering by platform 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-15 19:19:50 +00:00
ebanks 8f4bc8cb6e Move filtering functionality into the PrintReadsWalker. More to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-15 16:38:08 +00:00
kiran 0583459839 Another formatting change to make Hapmap sites more clearly visible. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1004 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-12 19:53:21 +00:00
kiran e9be2a9c60 Changed a formatting issue. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1002 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-12 19:40:32 +00:00
ebanks 032d0436e6 Added ROD for 1KG SNP calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@988 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 19:53:51 +00:00
ebanks ffffe3b2f6 -Support for 1KG SNP calls in RODs 
-Minor bug fix


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@987 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 18:56:37 +00:00
aaron 63b5c12cbd Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-11 18:13:22 +00:00
hanna 678ddd914f Stopgap fixes GFF, DbSNP being half-open rather than half-closed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 21:38:57 +00:00
aaron 94b0e46d12 checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 20:46:16 +00:00
aaron 72a81f8f25 removed the requirement that a bam file list be present in the XML version of the command line arguments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@975 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 20:01:13 +00:00
aaron f304803811 initial check-in of an easy way to create command line tools based on the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@970 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 17:34:02 +00:00
kiran b0cc763eb5 Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 17:31:00 +00:00
hanna ad80894afa Bumped picard to latest svn version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@965 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 14:36:34 +00:00
aaron ec2f015447 fixed a bunch of comments and license headers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@964 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 14:10:46 +00:00
hanna dc6a9ca196 Pooling resources to lower memory consumption. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 13:39:32 +00:00
kiran 3adb4239e4 Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 08:19:31 +00:00