gatk-3.8

History

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
..
java	Write a new tool for spliting reads that have N cigar string.	2014-01-01 22:21:36 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

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

java

Write a new tool for spliting reads that have N cigar string.

2014-01-01 22:21:36 -05:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00