update htsjdk to 2.21.0 #6250
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update htsjdk to 2.21.0 #6250
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change in UpdateVCFSequenceDictionary to prevent 0 length sequences
cmnbroad
reviewed
Nov 6, 2019
| dict.getSequences().stream() | ||
| .filter( s -> s.getSequenceLength() == SAMSequenceRecord.UNKNOWN_SEQUENCE_LENGTH) | ||
| .map(SAMSequenceRecord::getSequenceName) | ||
| .collect(Collectors.joining(","))); |
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Do you think we should use .limit(20) or something? There might be a lot...
| @@ -209,11 +211,22 @@ else if (hasReference()) { | |||
| if (resultDictionary == null || resultDictionary.getSequences().isEmpty()) { | |||
| throw new CommandLineException.BadArgumentValue( | |||
| String.format( | |||
| "The specified dictionary source has an empty or invalid sequence dictionary", | |||
| "The specified dictionary source has an empty or invalid sequence dictionary: %S", | |||
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Is the upper casing deliberate %S ?
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Upgrading htsjdk to 2.21.0.
This includes a change that relaxes restrictions on loading vcfs with sequence dictionaries that are missing lengths. This effected one of the tests which I changed a bit. We could also implement blanket ban on sequence dictionaries with missing lengths in our sequence dictionary validation code, but we currently allow them for sam/bam as far as I can tell and have tests that take them into account.