This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch master in repository bedtools.
commit 9509809235906e0924a60a9c38abd39075547d1e Author: nkindlon <[email protected]> Date: Tue Mar 4 14:22:24 2014 -0500 Fixed intersect bug so that bed query with Bam DB correctly gives bed output. Added unit test. --- src/utils/Contexts/ContextBase.cpp | 12 +++--------- test/intersect/test-intersect.sh | 11 ++++++++++- 2 files changed, 13 insertions(+), 10 deletions(-) diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp index adbc47a..16d2402 100644 --- a/src/utils/Contexts/ContextBase.cpp +++ b/src/utils/Contexts/ContextBase.cpp @@ -94,15 +94,9 @@ bool ContextBase::determineOutputType() { return true; } - //Otherwise, if there are any BAM files in the input, - //then the output should be BAM. - for (_i = 0; _i < (int)_files.size(); _i++) { - if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) { - setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE); - _bamHeaderAndRefIdx = _i; - _outputTypeDetermined = true; - return true; - } + //Otherwise, if the input is BAM, then the output is BAM + if (getFile(0)->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) { + setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE); } //Okay, it's bed. diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh index da0ba96..e6c2c67 100644 --- a/test/intersect/test-intersect.sh +++ b/test/intersect/test-intersect.sh @@ -446,7 +446,16 @@ echo \ "chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I11^I21^I345.7^Iwhy?^I+" > exp $BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -S | cat -t > obs check obs exp - rm obs exp +################################################################## +# Test that intersect of bed query with BAM DB gives Bed output. +################################################################## +echo " intersect.t37...\c" +echo \ +"chr1 10 20 a1 1 + +chr1 100 200 a2 2 -" > exp +$BT intersect -a a.bed -b a.bam > obs + + rm one_block.bam two_blocks.bam three_blocks.bam \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
