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gatk-3.8/java/src/org/broadinstitute/sting/utils
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hanna 6955b5bf53 Cleanup of the doc system, and introduce Kiran's concept of a detailed summary 
below the specific command-line arguments for the walker.  Also introduced
@help.summary to override summary descriptions if required.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2337 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-12 04:04:37 +00:00
..
bed GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
cmdLine Refactor the code I gave Eric yesterday to output command line arguments. 2009-12-10 18:57:54 +00:00
duplicates Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared). 2009-12-02 20:04:22 +00:00
fasta A bit of cleanup in preparation for Picard patch. 2009-12-08 16:09:04 +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 Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well. 2009-12-11 19:51:05 +00:00
help Cleanup of the doc system, and introduce Kiran's concept of a detailed summary 2009-12-12 04:04:37 +00:00
pileup Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method. 2009-12-10 21:11:42 +00:00
sam Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine. 2009-11-30 17:39:29 +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 More archiving (with permission from Andrey) plus a move to core. 2009-12-03 15:40:27 +00:00
BaseUtils.java Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate. 2009-12-07 14:26:27 +00:00
CircularArray.java More archiving (with permission from Andrey) plus a move to core. 2009-12-03 15:40:27 +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
GATKErrorReport.java comments for eric 2009-11-13 14:19:31 +00:00
GenomeLoc.java code cleanup and containsStartPosition function 2009-10-27 21:53:40 +00:00
GenomeLocParser.java Validates intervals against sequence dictionary header bounds. 2009-10-22 19:31:15 +00:00
GenomeLocSortedSet.java GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
GenotypeUtils.java intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles. 2009-10-23 06:31:15 +00:00
JVMUtils.java Refactor the code I gave Eric yesterday to output command line arguments. 2009-12-10 18:57:54 +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 Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 2009-11-16 02:41:20 +00:00
MergingIterator.java General purpose merging iterator implementation 2009-09-12 19:06:15 +00:00
PackageUtils.java New PackageUtils interferes with the packaging utility. Revert until Aaron and 2009-11-02 19:14:14 +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
PluginManager.java Allow users to directly specify filters from the command-line, applicable to 2009-11-10 18:40:16 +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
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
TextFormattingUtils.java Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions. 2009-12-11 21:59:55 +00:00
Utils.java minor code cleanup 2009-11-30 20:57:20 +00:00
WilcoxonRankSum.java Get rid of characters in the docs that aren't universally compatible with 2009-12-07 21:41:07 +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