Ami Levy-Moonshine 6da53aea09 Write a new tool for spliting reads that have N cigar string. ... For example, this tool can be used for processing bowtie RNA-seq data. Each read with k N-cigar elemments is plit to k+1 reads. The split is done by hard clipping the bases rest of the bases. In order to do it, few changes were introduced to some other clipping methods: - make a segnificant change in ClippingOp.hardClip() that prevent the spliting of read with cigar: 1M2I1N1M3I. - change getReadCoordinateForReferenceCoordinate in ReadUtil to recognize Ns create unitTests for that walker: - change ReadClipperTestUtils to be more general in order to use its code and avoid code duplication - move some useful methods from ReadClipperTestUtils to CigarUtils create integration test for that class small change in a comment in FullProcessingPipeline last commit: Address review comments: - move to protected under walkers/rnaseq - change the read splitting methods to be more readable and more efficiant - change (minor changes) some methods in ReadClipper to allow the changes in split reads - add (minor change) one method to CigarUtils to allow the changes in split reads - change ReadUtils.getReadCoordinateForReferenceCoordinate to include possible N in the cigar - address the rest of the review comments (minor changes) - fix ReadUtilsUnitTest.testReadWithNs acoording to the defult behaviour of getReadCoordinateForReferenceCoordinate (in case of refernce index that fall into deletion, return the read index of the base before the deletion). - add another test to ReadUtilsUnitTest.testReadWithNs - Allow the user to print the split positions (not working proparly currently)		2014-01-01 22:21:36 -05:00
..
commandline	Add ability to specify min/max required/recommended values for numeric arguments in the @Argument annotation	2013-12-18 18:09:08 -05:00
gatk	Fixed bug in the filtering of lifted over variants where a deletion at the end of a contig could cause it to error out.	2013-12-11 14:07:18 -05:00
jna	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
utils	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
BaseTest.java	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
ExampleToCopyUnitTest.java	Add a class-based DataProvider	2013-12-03 13:31:01 -05:00
MD5DB.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
MD5Mismatch.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
WalkerTest.java	Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy	2013-12-03 23:12:14 -05:00