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ChangeLog
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ChangeLog
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lobstr_v2.0.0 (July 18, 2012):
- added paired-end functionality (fastq, fasta, and bam)
- read from gzipped format
- partially spanning reads
- read from amazon S3
- improved mapping quality and confidence scores
- vcf format conversion
lobstr_v2.0.0_2 (August 1, 2012):
- fixed problem reading from paired-end bam files (reads were not properly reverse complemented)
lobstr_v2.0.1 (August 13, 2012):
- fixed invalid CIGAR string issue: some reads were clipped at the end but "S" was not added to the CIGAR string. Reads with "S" at the end of the CIGAR string are now treated as partially spanning
- changed PCR duplicate removal to only check that reads have the same start coordinate and orientation, rather than also checking that they are the same length. Read trimming causes reads with the same original length to have different lengths and therefore not be flagged properly as duplicates
- changed required stitch overlap score to be 0.1 above next best score
- check both forward and reverse complement when using IsPerfectRepeat function
- changed XG tag to say "NA" for partially spanning reads
lobstr_v2.0.2 (September 30, 2012):
- changed they way lobSTR checks input for paired-end BAM files. Instead of stripping /1 and /2 from ends of read, look for /1 and /2 anywhere in the read name and strip all characters after that.
- Fixed bug in indexing that reported some empty reference sequences that caused alignment to break when checking the fasta file.
- Added option --exclude-partial to avoid processing any partially spanning reads during allelotyping and alignment.
- changed --sex option to --haploid. Now, specify --haploid <comma-separated list fo chroms to treat as haploid>. To specify the whole organism as haploid, use --haploid all. Kept --sex option for compatibility with rest of lobstr 2 versions.
- added --rg option to add read group to alignments in BAM format
- changed mapquality to say 255, put alignment score in XQ tag
- added NM tag to BAM file
- fixed off-by-one error in reporting extracted STR sequence
- removed R dependency for allelotyping
lobstr_v2.0.2_1 (November 1, 2012):
- changed error in reporting coverage columns for paired end samples
- changed partial flag not to be set by default
lobSTR_v2.0.3 (February 1, 2012):
- Updated VCF format to be compatible with 1000 Genomes
- Allelotype now writes both .genotypes.tab and .vcf files, no need for lobstr_to_vcf.py.
- Allow for reading paired end bam files even when not all mates are present
lobSTR_v2.0.4 (February 27, 2013):
- Bug fixes:
- Problem reporting coverage values in the VCF that are twice as much as they should be
- Problem parsing tags from BAM files that have been modified after running lobSTR.
- Multithreading now does not create truncated bam files
- lobSTR can now compile on many more systems and the configuration setup has been cleaned up.
- Determining the STR allele supported by a read: in v2.0.3 and earlier, by default lobSTR attempted to
only include indels it determined to be inside of the STR region. This could be turned off by the --include-flank
option. In comparison to external datasets. In v2.0.4 this was changed so that by default, all indels
in the read are included, but it can be turned off using the --dont-include-flank option. This is described
on the FAQ page of the website.