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Commits : Listings

  Analyzed 5 days ago based on code collected 5 days ago.
Showing page 1 of 51
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Release 1.82 Anon32
alecw
More... 5 months ago
PIC-344. MarkDuplicates now adds PG records (chaining and uniquifying appropriately) by default. Anon32
alecw
More... 5 months ago
Add SAMLineParser getters. Anon32
alecw
More... 5 months ago
Refactor SAMTextReader to allow a String in SAM text format to be parsed independently by new class SAMLineParser. Anon32
alecw
More... 5 months ago
Adjusted quality format validation logic: only attempts to infer quality if records are available Anon32
mmccowan
More... 5 months ago
PIC-538 Fix bug in which setting maxRecordsInRam caused an exception when creating a BAM writer. Anon32
alecw
More... 5 months ago
Added utility for automatic detection of quality encodings of fastqs and bams; incorporated into FastqToSam so no format need be specified; incorporated into ValidateSamFile so that an warning is generated if the BAM is not Standard/Phred-encoded Anon32
mmccowan
More... 5 months ago
Allow null to be passed to any ctor arg. Anon32
alecw
More... 6 months ago
PIC-537 Speed up parsing of SAM header by avoiding throwing exception in non-exceptional situation in ISO-8601 date parser. Anon32
alecw
More... 6 months ago
PIC-537 Speed up parsing of SAM header by precompiling regexes and by using StringUtil.split rather than String.split. Anon32
alecw
More... 6 months ago
Release 1.81 Anon32
alecw
More... 6 months ago
Added TruSeq small RNA adapter sequences. Anon32
tfenne
More... 6 months ago
Improve javadoc for queryMate. Anon32
alecw
More... 6 months ago
Minor javadoc edit. Anon32
tfenne
More... 6 months ago
add padding to index portion of scattered directory names so that they are always 4 digits long Anon32
brilliantred
More... 6 months ago
Minor change to ProgressLogger to support things that are not SAMRecord. Anon32
tfenne
More... 6 months ago
Release 1.80 Anon32
alecw
More... 6 months ago
Bug fix: "-?" is now recognized as NaN Anon32
mmccowan
More... 7 months ago
Added constructor accepting generic TabbedInputParser Anon32
mmccowan
More... 7 months ago
Updated SamFileValidator to check for records that have no read group id, or that have a read group id that is not found in the header. Anon32
brilliantred
More... 7 months ago
 
 
 

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Creative Commons License Copyright © 2013 Black Duck Software, Inc. and its contributors, Some Rights Reserved. Unless otherwise marked, this work is licensed under a Creative Commons Attribution 3.0 Unported License . Ohloh ® and the Ohloh logo are trademarks of Black Duck Software, Inc. in the United States and/or other jurisdictions. All other trademarks are the property of their respective holders.