Mercurial > repos > blankenberg > naive_variant_detector
changeset 5:4a67169be0ee
Update to allow out of bounds positions to be not be fatal errors.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Thu, 16 May 2013 09:27:59 -0400 |
| parents | 1c23da12b768 |
| children | dbca9274b2e0 |
| files | dependency_configs/tool_dependencies.xml tools/naive_variant_detector.py tools/naive_variant_detector.xml |
| diffstat | 3 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/dependency_configs/tool_dependencies.xml Wed May 15 09:37:01 2013 -0400 +++ b/dependency_configs/tool_dependencies.xml Thu May 16 09:27:59 2013 -0400 @@ -3,9 +3,9 @@ <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb" /> </package> <package name="pyBamParser" version="0.0.1"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_pybamparser" owner="blankenberg" changeset_revision="7f55ab725342" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_pybamparser" owner="blankenberg" changeset_revision="3cbac77af20f" /> </package> <package name="pyBamTools" version="0.0.1"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_pybamtools" owner="blankenberg" changeset_revision="3b4a96996e8f" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_pybamtools" owner="blankenberg" changeset_revision="0b4fb804d717" /> </package> </tool_dependency>
--- a/tools/naive_variant_detector.py Wed May 15 09:37:01 2013 -0400 +++ b/tools/naive_variant_detector.py Thu May 16 09:27:59 2013 -0400 @@ -19,6 +19,7 @@ parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' ) parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' ) parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default='uint8', help='dtype to use for coverage array' ) + parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' ) parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' ) (options, args) = parser.parse_args() @@ -55,7 +56,7 @@ coverage = VCFReadGroupGenotyper( map( lambda x: Reader( *x ), bam_files ), options.reference_genome_filename, dtype=options.coverage_dtype, min_support_depth=options.min_support_depth, min_base_quality=options.min_base_quality, min_mapping_quality=options.min_mapping_quality, - restrict_regions=regions, use_strand=options.use_strand ) + restrict_regions=regions, use_strand=options.use_strand, allow_out_of_bounds_positions=options.allow_out_of_bounds_positions ) for line in coverage.iter_vcf( ploidy=options.ploidy, variants_only=options.variants_only ): out.write( "%s\n" % line ) out.close()