gatk-3.8

Commit Graph

Author	SHA1	Message	Date
Guillermo del Angel	5b6d279a2e	Two bug fixes: a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint. b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.	2011-06-29 10:21:27 -04:00
David Roazen	139c6b84a1	Modified build.xml and the help extractor doclet to use the output of "git describe" as an absolute version number (if the repository has at least one tag), using the raw SHA-1 hash value as a fallback version number in the case where there are no tags.	2011-06-28 08:37:05 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00

Author

SHA1

Message

Date

Guillermo del Angel

5b6d279a2e

Two bug fixes:

a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.

2011-06-29 10:21:27 -04:00

David Roazen

139c6b84a1

Modified build.xml and the help extractor doclet to use the output of "git

describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.

2011-06-28 08:37:05 -04:00

David Roazen

3c9497788e

Reorganized the codebase beneath top-level public and private directories,

removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.

2011-06-28 06:55:19 -04:00

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103 Commits (891c5d84d92209936a26af15be6d2220a6858675)