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release 1.19
- cope with unknown sort order in header
release 1.18
- new command line option CHANGE_RG_NAME default false
- NB this is a change to previous behaviour, where it was always true
release 1.17
- New command line option ADD_CLUSTER_INDEX_TAG default false
- Added function to read experiment name and computer name from runParameters file
used to generate read name prefix if config file does not exist, updated tests
- Ignore N's in barcode sequence when looking for matches, updated tests
release 1.16
- AlignmentFilterTest.java, testChimericReads -
- compare deeply the content of json files with
- org.codehaus.jackson.map.ObjectMapper,
- ignore the programVersion field
- Change all tabs to spaces
- Remove javac warning
- Fix separate tags for dual index runs and add tests
release 1.15
- ensure the readname does not start with :
- Illumina HiSeqX instruments: one loc file for all lanes and tiles, no config xml files in basecalls or intensities directories
- allow for absence of run id and instrument info in the configuration file
release 1.14
- AlignmentFilter now supports BAM/SAM files containing secondary and supplemental alignments
release 1.13
- Add BC_READ and SEC_BC_READ command line options to specify which reads the barcode tag and second barcode tag should be attached to
release 1.12
- handled EXCLUDE_UNALIGNED=true for xahuman in SplitBamByChromosomes
- use separate test directories test1/2/3 where threading can cause output file clashes e.g. AlignmentFilterTest
- merge tests where one test uses the output of another e.g. ChangeBamHeaderTest
release-1.11
- include PG field in new RG header records
- use Picard 1.96 rather than 1.84
- [Hinxton #354882] separate_y_chromosome_data
release-1.10
- bugfix for single fragment/read templates in AlignmentFilter
- use Picard 1.84
release-1.09
- allow cycle range by read to be specified on command line
release-1.08
- corrects compile errors which went undetected in 1.07
release-1.07
- adapted IlluminaFileReader to read either normal or gzip compressed files
release-1.06
- corrects errors in git tagging with 1.04 and 1.05
release-1.04
- new tool SplitBamByChromosomes
- Can split BAM output into "target" and "excluded" files based on chromosomes to which reads align. Chromosomes defined as entries in SQ list from BAM header.
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.