Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
*Still needs debugging because code is not working.
Created test classes to be used across several tests.
Some cases are still commented out.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Insertions are a problem so cigar cases with "I" are commented out.
The test works with multiple deletions and matches.
This is still not a complete test. A lot of cigar test cases are commented out.
Added insertions to ReadClipperUnitTest
ReadClipper now tests for all indels.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Turns out that someone previously upped the declared size of a ROD shard to 100M bases, making
each ROD shard larger than the size of chr20. Why didn't we see this in Stable? Because the
ShardStrategy/ShardStrategyFactory mechanism was dutifully ignoring the shard size specification.
When I rolled the ShardStrategy/ShardStrategyFactory mechanics back into the DataSources as part
of the async I/O project, I inadvertently reenabled this specifier.
PreQC parses file with spaces in sample names by using tabs only.
PostQC allows passing the file names for the evals so that flanks can be evaled.
BaseTest's network temp dir now adds the user name to the path so files aren't created in the root.
HybridSelectionPipeline:
- Updated to latest versions of reference data.
- Refactored Picard parsing code replacing YAML.
This has implications for both Qscript authors and CommandLineFunction authors.
Qscript authors:
You no longer need to (and in fact must not) manually escape String values to
avoid interpretation by the shell when setting up Walker parameters. Queue will
safely escape all of your Strings for you so that they'll be interpreted literally. Eg.,
Old way:
filterSNPs.filterExpression = List("\"QD<2.0\"", "\"MQ<40.0\"", "\"HaplotypeScore>13.0\"")
New way:
filterSNPs.filterExpression = List("QD<2.0", "MQ<40.0", "HaplotypeScore>13.0")
CommandLineFunction authors:
If you're writing a one-off CommandLineFunction in a Qscript and don't really
care about quoting issues, just keep doing things the direct, simple way:
def commandLine = "cat %s | grep -v \"#\" > %s".format(files, out)
If you're writing a CommandLineFunction that will become part of Queue and
will be used by other QScripts, however, it's advisable to do things the
newer, safer way, ie.:
When you construct your commandLine, you should do so ONLY using the API methods
required(), optional(), conditional(), and repeat(). These will manage quoting
and whitespace separation for you, so you shouldn't insert quotes/extraneous
whitespace in your Strings. By default you get both (quoting and whitespace
separation), but you can disable either of these via parameters. Eg.,
override def commandLine = super.commandLine +
required("eff") +
conditional(verbose, "-v") +
optional("-c", config) +
required("-i", "vcf") +
required("-o", "vcf") +
required(genomeVersion) +
required(inVcf) +
required(">", escape=false) + // This will be shell-interpreted
required(outVcf)
I've ported the Picard/Samtools/SnpEff CommandLineFunction classes to the new
system, so you'll get free shell escaping when you use those in Qscripts just
like with walkers.
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
Also includes convenience parameters for specifying the IO/CPU threading balance outside of a tag. Will be killed when
Queue gets better support for tagged arguments (hopefully soon).
-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./. Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values. There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.
A UserException is now thrown if someone tries to use this syntax.
-- Now you provide a LazyParsing object
-- LazyGenotypesContext now knows nothing about the VCF parser itself. The parser holds all of the necessary data to parse the VCF genotypes when necessarily, and the LGC only has a pointer to this object
-- Using new interface added LazyGenotypesContext to unit tests with a simple lazy version
-- Deleted VCFParser interface, as it was no longer necessary
-- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading.
-- This new class was replaced all of the old, complex functionality
-- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency. This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily
-- Misc. bug fixes throughout the system
-- Bug fixes for PhaseByTransmission with new GenotypesContext
Eric Banks
Mauricio Carneiro
Roger Zurawicki
Laurent Francioli
Guillermo del Angel
Mark DePristo
Matt Hanna
Khalid Shakir
David Roazen
Ryan Poplin