Implemented a mixin called "RetryMemoryLimit" which will by default double the memory.
GridEngine memory request parameter can be selected on the command line via '-resMemReqParam mem_free' or '-resMemReqParam virtual_free'.
Java optimizations now enabled by default:
- Only 4 GC threads instead of each job using java's default O(number of cores) GC threads. Previously on a machine with N cores if you have N jobs running and java allocates N GC threads by default, then the machines are using up to N^2 threads if all jobs are in heavy GC (thanks elauzier).
- Exit if GC spends more than 50% of time in GC (thanks ktibbett).
- Exit if GC reclaims lest than 10% of max heap (thanks ktibbett).
Added a -noGCOpt command line option to disable new java optimizations.
Updated HSP to use new padding arguments instead of flank intervals file, plus latest QC evals.
IntervalUtils return unmodifiable lists so that utilities don't mutate the collections.
Added a JavaCommandLineFunction.javaGCThreads option to test reducing java's automatic GC thread allocation based on num cpus.
Added comma to list of characters to convert to underscores in GridEngine job names so that GE JSV doesn't choke on the -N values.
JobRunInfo handles the null done times when jobs crash with strange errors.
-- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller
-- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers
-- VCF parsers now automatically repair standard VCF header lines when reading the header
-- Updating integration tests to reflect header changes
-- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test
-- SelectHeaders now always updates the header to include the contig lines
-- SelectVariants add UG header lines when in regenotype mode
-- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY
-- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs)
-- Throw error when VCF has unbounded non-flag values that don't have = value bindings
-- By default we no longer allow writing of BCF2 files without contig lines in the header
-- This file is in integrationtests/md5mismatches.txt, and looks like:
expected observed test
7fd0d0c2d1af3b16378339c181e40611 2339d841d3c3c7233ebba9a6ace895fd test BeagleOutputToVCF
43865f3f0d975ee2c5912b31393842f8 1b9c4734274edd3142a05033e520beac testBeagleChangesSitesToRef
daead9bfab1a5df72c5e3a239366118e 27be14f9fc951c4e714b4540b045c2df testDiffObjects:master=/local/dev/depristo/itest/public/testdata/diffTestMaster.vcf,test=/local/dev/depristo/itest/public/testdata/diffTestTest.vcf,md5=daead9bfab1a5df72c5e3a239366118e
-- Associated cleanup with making md5db an instantiated object, rather than a bunch of static methods
The practical differences between version 1.0 and this one (v1.1) are:
* the underlying data structure now uses arrays instead of hashes, which should drastically reduce the memory overhead required to create large tables.
* no more primary keys; you can still create arbitrary IDs to index into rows, but there is no special cased primary key column in the table.
* no more dangerous/ugly table operations supported except to increment a cell's value (if an int) or to concatenate 2 tables.
Integration tests change because table headers are different.
Old classes are still lying around. Will clean those up in a subsequent commit.
- By porting from jython to java now accessible to Queue via automatic extension generation.
- Better handling for problematic sample names by using PicardAggregationUtils.
GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name.
CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering.
Added SelectHeaders walker for filtering headers for dbGAP submission.
Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter.
Latest WholeGenomePipeline.
Other minor cleanup to utility methods.
- The Integer column type now accepts byte and shorts
- Updated Unit Tests and added a new testParse() test
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
QScript accessor to QSettings to specify a default runName and other default function settings.
Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs.
Gathered log files concatenate all log files together into the stdout.
InProcessFunctions now have PrintStreams for stdout and stderr.
Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml.
During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file.
In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope.
Added more detailed output when running with -l DEBUG.
Simplified graphviz visualization for additional debugging.
Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List)
Minor cleanup to build including sending ant gsalib to R's default libloc.
Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory.
Updated various tests for above items and other small fixes.
* Added standard pipeline test for the DPP
* Added a full BWA pipeline test for the DPP
* Included the extra files for the reference needed by BWA (to be used by DPP and PPP tests)
* added a pipeline test to the Pacbio Processing Pipeline.
* updated exampleBAM with more complete RG information so we can use it in a wider variety of pipeline tests
* added exampleDBSNP.vcf file with only chromosome 1 in the range of the exampleFASTA.fasta reference for pipeline tests
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.
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
- Ability to pass a different resident memory reservation and limits. Useful for large pileups of low pass genome data that sometimes need high -Xmx6g but usually don't exceed 2-3g in actual heap size.
- Fixed jobPriority to work for all job runners. Now must be a integer between 0 and 100- even for GridEngine- and will be mapped to the correct values.
- Passing parallel environment and job resource requests to LSF and GridEngine. Useful for passing tokens like iodine_io=1 and -pe pe_slots 8
- Refactored GridEngine JobRunner to also provide basic support for other job dispatchers with DRMAA implementations such as Torque/PBS. Should work for basic running but advanced users must pass their own jobNativeArgs from the command line or in customized QScripts until someone maps properties like jobQueue, jobPriority, residentRequest, etc. into a Torque/PBS/etc. dispatcher.
- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
Khalid Shakir
Eric Banks
Mauricio Carneiro
Mark DePristo
Roger Zurawicki
David Roazen