(-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.
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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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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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- changed to a better method for getting headers from Codecs
- some removal of old commented out code in the GATKAgrumentCollection
- changes for the rename of FeatureReader to FeatureSource
- removed the old Beagle ROD
- cleaned up some of the code in SampleUtils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3826 348d0f76-0448-11de-a6fe-93d51630548a
- Remove some old debugging cruft regarding handling of threaded engine exceptions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3796 348d0f76-0448-11de-a6fe-93d51630548a
impacts performance on low-pass data and, if it works well, will create a more automatic version of the tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3709 348d0f76-0448-11de-a6fe-93d51630548a
are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
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as walker attributes or from the command-line. Not ready yet! Downsampling/deduping
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
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hanna
kshakir
depristo
aaron
ebanks
asivache