Also added the old model of indel calling to the FCP.
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Using the VCFWriterATD isCompressed to check if the VCF index will be auto generated.
Tracking BAM and Tribble indexes as @Inputs and @Outputs in generated QFunctions.
Updates to the BamGatherFunction to disable the index during merge when disable_bam_indexing = true.
Made a shortcut for live-running pipelinetest, pipelinetestrun.
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extracted from source files that have been modified since the help resource
file was last generated. This significantly speeds up builds where only a few
source files have been modified, at the expense of making clean builds take
slightly longer. Here's some performance data gathered by testing the old and
new versions of extracthelp in isolation and averaging across 10 runs:
old extracthelp, 1 modified source file: 20.1 seconds
new extracthelp, 1 modified source file: 7.2 seconds <-- woohoo! :)
old extracthelp, clean build: 17.8 seconds
new extracthelp, clean build: 20.5 seconds
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Custom gatherer prints out the class name in the logs.
Try to retrieve mail domain from /etc/mailname before falling back to the hostname.
Building oneoff jars during ant oneoffs.
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Added a property to allow generating Queue extensions around an external version of the GATK.
Updated argument order in -help.
Restored the ability to use QScript trait imported annotations in constructors.
Removing line feeds from email password files.
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Added an empty wrapper for a GridEngine job runner which is only activated when SGE_ROOT is detected.
Refactored a bit more common code into CommandLineJobRunner / JobRunner / FunctionEdge.
Status for analyisNames now includes the number of functions in state.
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directory to live anywhere on the filesystem.
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functionality for BAM index visualization.
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GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
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Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
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Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
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When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
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dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
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- Add StingTextReporter, which provides a text dump of the errors to the
console. Had to create our own reporter (inheriting from the standard
TestNG TextReporter) to work around a configuration issue with the
TextReporter. In an ideal world, I'd report this on the TestNG mailing
list and help them resolve the issue, but this solution is relatively
robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
file.
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Initial test to see how Bamboo will respond. More detailed email to follow.
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of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.
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Shell invoking scripts so that even really long shell scripts make it through LSF.
Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs.
Switched the default from re-running everything to re-running only files that need to be regenerated. --skip_up_to_date replaced with --start_clean for those who want to regenerate everything.
Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions. (40s for a 100 function graph exploding to a 2500 function graph)
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Will see how this behaves for those using IntelliJ as generated source code will disappear during an ant clean.
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1) Build the module with the following command:
$ ant gsalib
2) Add the module path to your ~/.Rprofile file:
.libPaths("/path/to/Sting/trunk/R/")
3) At the top of each R script that will use the library, include the line:
library(gsalib)
You can now use the package like any other R package. To get high-level documentation, supply the following command to R:
help(gsalib)
The methods contained herein are:
getargs : A method to easily provide arguments to interactive and non-interactive scripts.
Prints out a help message specifying how the script should be run if no arguments
or "-h" is provided. Very helpful when you're writing an R-script piecemeal in
interactive mode, then want to make it a command-line program.
plot.venn : Plots a two-way or three-way proportional Venn diagram.
read.eval : Reads VariantEval output that's formatted in R style.
read.gatkreport : Reads GATKReport output.
gsa.message : Emits a message with the prefix "[gsalib]" to stdout.
gsa.warn : Emits a warning message with the prefix "[gsalib] Warning:" to stdout.
gsa.error : Emits an error message with the prefix "[gsalib] Error: to stdout, calls traceback()
and halts execution.
Documentation on each of these methods can be obtained by typing "help(method_name)" at the R prompt.
* Retired GATKReport.R, as that functionality has now been moved to gsalib.
* Retired gsacommons, as that functionality has been split between gsalib and VariantReport.R.
* Modified VariantReport.R to make use of gsalib. The script now uses the getargs() method to provide the user with some information as to the proper way to run the script. Documentation on how to prepare output is given at http://www.broadinstitute.org/gsa/wiki/index.php/VariantEval .
* Added 'gsalib' target to build.xml file. Running "ant gsalib" will compile this module and place the R-ready package in R/gsalib .
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memory isn't being freed correctly when multiple integration tests run as
part of a single class.
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- Unit/integration test against the jars built to the dist directory, so that
the tests reveal classes that don't exist in the final jars.
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
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Some refactoring of Queue extensions for reusability in scripts.
Putting the extensions into the Queue.jar after building them.
More updates to GATK walker arguments specifying @Input and @Output for Queue.
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-l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run.
More documentation in the examples with a new even simpler CountReads example.
Took out unused option to build Queue GATK extensions separately.
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To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar.
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Added ability to skip up-to-date jobs where the outputs are older than the inputs.
Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names.
Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile
Moved Hidden from the GATK to StingUtils.
Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7
Added Queue to javadoc and testing build targets.
Added first Queue unit test.
Another pass at avoiding cycles in the DAG thanks to all function I/O being files.
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Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
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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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object or by a single object and all the references it contains. Requires a command-line change to add a Java agent to
the command-line; see the Sizeof.java javadoc for details.
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Modified build script so that queue is cleaned during "ant clean".
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Current version only has syntatic sugar for accessing the graph via rules ex. "bam" -> "bam.bai", "samtools index ${bam}" and DOES NOT have sugar for constructing your own graph.
Usage info on the internal wiki at https://iwww.broadinstitute.org/gsa/wiki/index.php/Queue
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
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for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature.
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won't aren't impacted when building the GATK from outside the base directory.
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more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
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You can tell ant not to halt with: 'ant -Dhalt=no' (yes is the default)
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
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out how do deal with the playground jar.
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ant -Ddist=altDist
or
ant -Ddist=/where/you/want/jars
Also changed the test build to depend on playground build instead of core, right now tests fail if you only build the core.
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Omit inner classes from the fileset of tests to run.
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example:
ant test -Dsingle=TraverseReadsTest
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(yet) deal elegantly with even simple cases.
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kshakir
droazen
depristo
kcibul
hanna
kiran
asivache
aaron
ebanks
jmaguire
rpoplin