carneiro 5e9a8f9cb3 Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base. ... 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		2011-01-05 22:25:08 +00:00
..
BoundedReadIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
BufferingReadIterator.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
DownsampleIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
GenomeLocusIterator.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
IterableIterator.java	Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.	2009-11-25 03:51:41 +00:00
LocusIterator.java	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
LocusIteratorByState.java	Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.	2010-11-19 19:59:05 +00:00
LocusIteratorFilter.java	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +00:00
NullSAMIterator.java	Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.	2010-09-25 02:49:30 +00:00
PeekingIterator.java	added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.	2009-06-16 22:15:56 +00:00
PositionTrackingIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
PushbackIterator.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
ReadFormattingIterator.java	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00
StingSAMIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
StingSAMIteratorAdapter.java	Moving StingException	2010-09-12 14:34:15 +00:00
VerifyingSamIterator.java	Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time	2010-12-04 20:23:06 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00