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v1.0.0

  • first public release

v1.1.0

  • added --simple option to report genotype result for each repeat locus on a single line as an alternative output format
  • fixed setup.py and requirements.txt to make sure pip install using Github URL works

v1.1.1

  • bugfix in tre.py

v1.2.0

  • bugfix: forgot to pass reads_fasta to extract_missed_clipped()
  • bugfix: min_support checking should use "greater than or equal to"
  • removed dependency on intspan
  • reduced min_len from 20 to 15 for comparing motifs using blastn
  • bugfix: keep track of genomic coordinates of all alignments to detect reads that truly span long reference repeats
  • assigned min_span explicitly in conditional instead of relying on initialized value - min_span does not change in some cases when runing genome scan for some unknown reason
  • added check_same_pats() in is_same_repeat() to check if one motif is subsequence of another in blastn matches
  • test data added
  • output BED file by default in addition to TSV (user provide output prefix instead of name). BED output simplied without details such as read names.
  • added --regions to specify (in BED format) specific regions for scanning
  • added --min_cluster_size (default=2) to separate from --min_support so that alleles with fewer read support can be segregated
  • remove optional usage of dbscan for clustering
  • improve boundary definition of long(kb range) repeat loci in genome scan
  • added --tmpdir to allow user to specify TEMP location for generating tmp files
  • allowed --min_cluster_size to be bigger than --min_suport for genotyping mode only

v1.3.0

  • strand column added to .tsv output to indicated strand of support read, read_start is recalculated based on read instead of alignment coordinate for negative strand sequences
  • blastn jobs deployed per locus for compareing target and detected motifs combined to one job per process
  • minimum coverarge, percent identity, and e-value added to blastn jobs when launched
  • when searching for repeat in insertion site, target_flank increased from 2000 to 3000
  • bedtools merge parameter d for merging detected insertion loci increased from 50 to 100
  • reads identified as clipped at repeat locus will not be examined again for same locus as if it is a full alignment
  • complete removal of temporary bed files unless --debug specified
  • straglr_compare.py added for comparing straglr results from test against control samples
  • Python3.8 now needed becasuse Scipy1.8 is needed for t-test in straglr_compare.py
  • new parameter trf_args to allow user specify his own preferred TRF settings
  • changed seeding method of Gaussian Mixture Model to "k-means++" to reduce CPU overhead
  • --working_directory added to allow user specify working directory, otherwise current directory will be used