(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
most appropriate based on feature density, and the longest feature in the file. Also:
- Converted Tribble to TestNG; it has better features and is about 6x faster.
- As much code clean-up as I could get done. More to do, especially in the example code.
- Moved asserts in the code to throw exceptions.
- Added getBinSize to the index interface; both indexes already implemented this.
- Removed the abstract parts of the indexCreator interface; this is now more simple.
- Added an IndexType enumeration; might be overkill but it is at least a single point of entry for index information.
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-o/--out instead of -varout. Let's watch as our intrepid support engineer
gracefully responds to all the incoming questions of the form: "the GATK told
me to use -o instead of -varout. What do I do?"
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Thanks to Matt for the advice.
Also, for Guillermo: while I was at it, I changed the .stats debug output to emit the original interval instead of the cleaned region.
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- Eliminate reduncancy of filter application.
- Track filter metrics per-shard to facitate per merging.
- Flatten counting iterator hierarchy for easier debugging.
- Rename Reads class to ReadProperties and track it outside of the Sting iterators.
Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics
classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking
the reads data source to manage the metrics; in the future, something more general should manage the metrics classes.
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Major cleanup of the genotype writer code from the calling end. UG no longer supports making calls in anything but VCF, and that allows us to use the VCFWriter more generically now. Putting the ball in Matt's court to finish collapsing everything.
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2) Small fixes in the VCFWriter:
a) Trailing missing values weren't being removed if their count was > 1 (e.g. ".,.")
b) We were handling key values that were Lists, but not Arrays. We now handle both.
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- Tribble is included directly in the GATK repo; those who have access to commit to Tribble can now directly commit from the GATK directory from Intellij; command line users can commit from
inside the tribble directory.
- Hapmap ROD now in Tribble; all mentions have been switched over.
- VariantContext does not know about GenomeLoc; use VariantContextUtils.getLocation(VariantContext vc) to get a genome loc.
- VariantContext.getSNPSubstitutionType is now in VariantContextUtils.
- This does not include the checked-in project files for Intellij; still running into issues with changes to the iml files being marked as changes by SVN
I'll send out an email to GSAMembers with some more details.
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Generalized some of the packaging code from VariantAnnotator. Matt might want to take a look to make this nicer...?
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b) Cosmetic change to Beagle annotation description.
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- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a
ebanks
rpoplin
hanna
aaron
kiran
depristo
delangel