gatk-3.8

History

Valentin Ruano-Rubio 96073c3058 This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK. The previous behavior is to process reads with N CIGAR operators as they are despite that many of the tools do not actually support such operator and results become unpredictible. Now if the there is some read with the N operator, the engine returns a user exception. The error message indicates what is the problem (including the offending read and mapping position) and give a couple of alternatives that the user can take in order to move forward: a) ask for those reads to be filtered out (with --filter_reads_with_N_cigar or -filterRNC) b) keep them in as before (with -U ALLOW_N_CIGAR_READS or -U ALL) Notice that (b) does not have any effect if (a) is enacted; i.e. filtering overrides ignoring. Implementation: * Added filterReadsWithMCigar argument to MalformedReadFilter with the corresponding changes in the code to get it to work. * Added ALLOW_N_CIGAR_READS unsafe flag so that N cigar containing reads can be processed as they are if that is what the user wants. * Added ReadFilterTest class commont parent for ReadFilter test cases. * Refactor ReadGroupBlackListFilterUnitTest to extend ReadFilterTest and push up some functionality to that class. * Modified MalformedReadFilterUnitTest to extend ReadFilterTest and to test the new filter functionality. * Added AllowNCigarMalformedReadFilterUnittest to check on the behavior when the unsafe ALLOW_N_CIGAR_READS flag is used. * Added UnsafeNCigarMalformedReadFilterUnittest to check on the behavior when the unsafe ALL flag is used. * Updated a broken test case in UnifiedGenotyperIntegrationTest resulting from the new behavior. * Updated EngineFeaturesIntegrationTest testdata to be compliant with new behavior	2013-06-10 10:44:42 -04:00
..
net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.	2013-06-10 10:44:42 -04:00

Valentin Ruano-Rubio 96073c3058 This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.

The previous behavior is to process reads with N CIGAR operators as they are despite that many of the tools do not actually support such operator and results become unpredictible.

Now if the there is some read with the N operator, the engine returns a user exception. The error message indicates what is the problem (including the offending read and mapping position) and give a couple of alternatives that the user can take in order to move forward:

a) ask for those reads to be filtered out (with --filter_reads_with_N_cigar or -filterRNC)

b) keep them in as before (with -U ALLOW_N_CIGAR_READS or -U ALL)

Notice that (b) does not have any effect if (a) is enacted; i.e. filtering overrides ignoring.

Implementation:

* Added filterReadsWithMCigar argument to MalformedReadFilter with the corresponding changes in the code to get it to work.
* Added ALLOW_N_CIGAR_READS unsafe flag so that N cigar containing reads can be processed as they are if that is what the user wants.
* Added ReadFilterTest class commont parent for ReadFilter test cases.
* Refactor ReadGroupBlackListFilterUnitTest to extend ReadFilterTest and push up some functionality to that class.
* Modified MalformedReadFilterUnitTest to extend ReadFilterTest and to test the new filter functionality.
* Added AllowNCigarMalformedReadFilterUnittest to check on the behavior when the unsafe ALLOW_N_CIGAR_READS flag is used.
* Added UnsafeNCigarMalformedReadFilterUnittest to check on the behavior when the unsafe ALL flag is used.
* Updated a broken test case in UnifiedGenotyperIntegrationTest resulting from the new behavior.
* Updated EngineFeaturesIntegrationTest testdata to be compliant with new behavior

2013-06-10 10:44:42 -04:00

net/sf/samtools

Delete unused FastaSequenceIndexBuilder class and accompanying test

2013-05-01 01:02:01 -04:00

org/broadinstitute/sting

This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.

2013-06-10 10:44:42 -04:00