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release-1.03
- read both tile list and range
release-1.02
- remove dist for github
- new tool BamAdapterFinder
- add bcel jar file in lib
release-1.01
- add program information in AlignmentFilter metrics file
release-1.00
- reorganise java class files with prefix uk.ac.sanger.npg in the package names.
- rewrite ant build file, add version number in the jar files and generate command options for each tool with java doc.
- remove version number dependency in tests.
- Picard updated from 1.67 to 1.68.
- AlignmentFilter: record reference SQ list in the metrics file.
release-0.04
- BamMerger allows extra reads in unmapped bam file and an option to add them to merged bam file, and merge flag information as well.
- read locs files if clocs file not available.
- allow one of Basecall and Intensity config xml file missing, try to use runParameters and RunInfo xml as well.
- new tools: BamIndexDecoder, SplitBamByReadGroup, AlignmentFilter, ChangeBamHeader, BamTagStripper and BamQualityQuantisation.
release-0.03
- cope with old format of filter file - no empty four bytes and version number in the header.
- try to find filter file from base call directory if not in base call lane directory.
- use pos file if no clocs file found.
- cope with config xml file when using bustard directory as base call directory.
release-0.02
- a new BamReadTrimmer tool added to strip part of a read (fixed position) - typically a prefix of the forward read, and optionally place this and its quality in BAM tags.
- a new BamMerger tool added to merge BAM/SAM alignment info in a bam with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM. The SQ records and alignment PG records in the aligned bam file will be added to the header of unmampped bam file to form the new header of output file.
- stop using decimal format for position coordinates to improve clocs file reading.
- use BufferedInputStream for file input streams to improve file reading speed.
- set default timezone to a fixed timezone GMT in order for the run start date fixed in test sam/bam file.