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gatk-3.8/java/src/org/broadinstitute/sting/utils
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chartl 3b1fabeff0 Major code refactoring: 
@ Pooled utils & power
   - Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
     flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
   - Removed a number of PoolUtils variables and methods that were used in those walkers or simply
     not used
   - Removed AnalyzePowerWalker (un-necessary)
   - Changed the location of Quad/Squad/ReadOffsetQuad into poolseq

@NQS
   - Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType

@ BaseTransitionTable
   - Added a slew of new integration tests for different flaggable and integral parameters
   - (Scala) just a System.out that was added and commented out (no actual code change)
   - (Java) changed a < to <= and a boolean formula


Chris



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-10-20 14:58:04 +00:00
..
bed GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
cmdLine Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces 2009-10-15 12:07:44 +00:00
containers Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 2009-10-20 12:23:36 +00:00
duplicates Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes. 2009-07-06 15:41:30 +00:00
fasta Bumping version of Picard for firehose compatibility. 2009-10-16 19:38:56 +00:00
fastq Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity. 2009-09-03 17:20:16 +00:00
genotype VCF output now emits no calls as ./. 2009-10-16 18:51:31 +00:00
io Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 2009-10-20 12:23:36 +00:00
sam General-purpose management of output streams. 2009-08-23 00:56:02 +00:00
threading Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
AlignmentUtils.java the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked) 2009-09-14 16:04:19 +00:00
BaseUtils.java simpleComplement function() in BaseUtils. Generic framework for clipping reads along with tests. Support for Q score based clipping, sequence-specific clipping (not1), and clipping of ranges of bases (cycles 1-5, 10-15 for example). Can write out clipped bases as Ns, quality scores as 0s, or in the future will support softclipping the bases themselves. 2009-10-16 22:29:35 +00:00
BasicPileup.java @BasicPileup - made the counts public so they can be used 2009-10-16 21:56:56 +00:00
ComparableSAMRecord.java only compare pair position for paired end reads 2009-07-08 04:07:08 +00:00
ExpandingArrayList.java Now uses expanding array list for coverage histograms. No hard limit on maximum depth now 2009-09-16 23:27:25 +00:00
GenomeLoc.java Easier to print GenomeLoc compareTo() 2009-09-12 19:10:35 +00:00
GenomeLocParser.java fixed a bug I checked in that Eric found, for intervals with no start or stop coordinate. Now I owe Eric a cookie, and Milk Street is so far away. Damn. 2009-09-22 04:34:18 +00:00
GenomeLocSortedSet.java GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
GenotypeUtils.java Removing the AllelicVariant interface, which is replaced by the Variation interface. 2009-10-06 17:44:24 +00:00
JVMUtils.java Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 2009-09-29 22:23:19 +00:00
ListUtils.java Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass. 2009-09-28 18:12:32 +00:00
MalformedGenomeLocException.java A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu 2009-06-02 18:14:46 +00:00
MathUtils.java @ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0. 2009-08-27 19:31:53 +00:00
MergingIterator.java General purpose merging iterator implementation 2009-09-12 19:06:15 +00:00
PackageUtils.java Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00
Pair.java The building blocks for segmenting covariate counting data by read group. 2009-06-04 19:55:24 +00:00
PathUtils.java Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm. 2009-05-21 19:31:54 +00:00
Pileup.java General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool. 2009-04-14 22:13:10 +00:00
Predicate.java Push core / playground lower into the tree. 2009-03-23 23:19:54 +00:00
PrimitivePair.java Push core / playground lower into the tree. 2009-03-23 23:19:54 +00:00
QualityUtils.java Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 2009-08-28 14:14:21 +00:00
ReadBackedPileup.java Major code refactoring: 2009-10-20 14:58:04 +00:00
SWPairwiseAlignment.java -set indel cleaning walkers to be in core package 2009-07-24 05:23:29 +00:00
StingException.java Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it. 2009-04-29 22:09:41 +00:00
Utils.java All walkers now use read.getReadGroup() 2009-10-14 19:27:40 +00:00
package.html Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
xReadLines.java Documentation and cleanup of xReadLines. 2009-03-25 15:36:21 +00:00