let's align two sequences (shown below, good alignment)
AAATTTGGTAAAA-GT
AAATTTGGTAAAAGGT
now let's reverse the same very sequences and align again
TGAAAATGGTTTAAA
TGGAAAATGGTTTAAA
Note how we lost the deletion and got a mismatch instead at the very first letter of the upper sequence. The overall score of any particular alignment does not depend on the direction of the traversal, so the best alignment (with the highest score) should stay the same too.
New version fixes this issue and produces correct alignment of reverse sequences (up to the different choice of redundant position for the deletion):
T-GAAAATGGTTTAAA
TGGAAAATGGTTTAAA
This version also has the main() method reinstated, so the aligner can be run on its own as a little app.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5255 348d0f76-0448-11de-a6fe-93d51630548a
svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
shard merging algorithm. Tried to leave most of the building blocks in
Picard. If this turns into a logistical nightmare, I'll merge the building
blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
better separation of query and management functionality for reads, ref, rmd,
and samples.
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
reads package, indicating it's current strong relationship with the reads,
rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
the mysterious failure in STING_INTEGRATION-3832, the next time it appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5164 348d0f76-0448-11de-a6fe-93d51630548a
Moved the BamListWriter from FCP to ListWriterFunction in the Queue core.
Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s.
Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a
- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
out the non-deterministic VariantEvalIntegrationTest errors we've been seeing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4995 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
streaming/piping VCFs into the GATK. Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build
RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
are the walkers that feel the need to access the ROD system directly. (We need to stamp out
this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs. These'll be
fixed as part of the VCF streaming project.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default.
Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call.
Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a
subjected to and passes cursory testing on one dataset (and all integration tests pass).
However, there's a small library of validation checks, and unit and integration tests
that must be added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4813 348d0f76-0448-11de-a6fe-93d51630548a
BAQ has generally useful improvements. Refactor code to make it easier for BAQUnitTest to run. minBaseQuality enforced on output, as well as input now. Added BAQUnitTest that checks that the BAQ calculation is performing as expected. Still needs to be expanded significantly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4804 348d0f76-0448-11de-a6fe-93d51630548a
SAMFileWriterStub now supports BAQ writing as an internal feature. Several walkers have the @BAQMode applied to this, with parameters that I think are reasonable. Please look if you own these walkers, though
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4798 348d0f76-0448-11de-a6fe-93d51630548a
Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
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.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4683 348d0f76-0448-11de-a6fe-93d51630548a
Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode)
NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a
- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
1: -sample can now include a file, which will be parsed for sample-name entries
2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out
3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise)
4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad)
There is a legacy comparison object which is unused which I will strip out soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4502 348d0f76-0448-11de-a6fe-93d51630548a
by the fact that the GATKSAMRecord, by design, needs to both inherit from
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.
Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation. But in
the short-term, there's no obvious fix.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
depristo
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