# HG changeset patch # User lparsons # Date 1397246514 14400 # Node ID d5edaf8dc97432749a5c4f761e82e554876f00fb # Parent 227f9d3f0e323f259f67e828e023c3c4e0bde5b4 Fixed test output, added missing pysam dependency diff -r 227f9d3f0e32 -r d5edaf8dc974 htseq-count.xml --- a/htseq-count.xml Fri Apr 11 15:05:28 2014 -0400 +++ b/htseq-count.xml Fri Apr 11 16:01:54 2014 -0400 @@ -1,10 +1,11 @@ - + - Count aligned reads in a BAM file that overlap features in a GFF file htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/' numpy htseq samtools + pysam ##set up input files diff -r 227f9d3f0e32 -r d5edaf8dc974 test-data/htseq-test-paired_othercounts.tsv --- a/test-data/htseq-test-paired_othercounts.tsv Fri Apr 11 15:05:28 2014 -0400 +++ b/test-data/htseq-test-paired_othercounts.tsv Fri Apr 11 16:01:54 2014 -0400 @@ -1,5 +1,5 @@ -no_feature 533 -ambiguous 1 -too_low_aQual 0 -not_aligned 0 -alignment_not_unique 0 +_feature 755 +__ambiguous 0 +__too_low_aQual 96 +__not_aligned 0 +__alignment_not_unique 0 diff -r 227f9d3f0e32 -r d5edaf8dc974 test-data/htseq-test_othercounts.tsv --- a/test-data/htseq-test_othercounts.tsv Fri Apr 11 15:05:28 2014 -0400 +++ b/test-data/htseq-test_othercounts.tsv Fri Apr 11 16:01:54 2014 -0400 @@ -1,5 +1,5 @@ -no_feature 19 -ambiguous 0 -too_low_aQual 0 -not_aligned 1336 -alignment_not_unique 0 +__no_feature 19 +__ambiguous 0 +__too_low_aQual 0 +__not_aligned 1336 +__alignment_not_unique 0 diff -r 227f9d3f0e32 -r d5edaf8dc974 tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 11 15:05:28 2014 -0400 +++ b/tool_dependencies.xml Fri Apr 11 16:01:54 2014 -0400 @@ -9,6 +9,10 @@ + + + +