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STAR-SEQR 0.1.1:
  • STAR-SEQR is now compatible with Py3
  • Travis CI for python versions 2.7, 3.4, 3.5
  • Checks to ensure primer design targets are compatible w/seq length
  • Annotation field is now ordered by junction dist, cdslen and transcript name for consistency
STAR-SEQR 0.2.0:
  • The smallest portion of a split read is now used to calculate number of frags >20 as MINFRAG20 or MINFRAG35
  • More filters are applied to remove FPs with certain read characteristics such as diversity, MINFRAG20, and Cross-Homology
  • Candidate info has been converted to not contain nested lists
  • New output format with more info
STAR-SEQR 0.2.1:
  • Added a script for making a DREAM challenge compliant bedpe
STAR-SEQRv0.2.2:
  • Change absolute path requirements for gtf and fasta to accomodate docker
STAR-SEQRv0.2.3:
  • Changed all realpath statements to abspath.
STAR-SEQRv0.2.4:
  • Updated to work with pandas 19.2 and numpy 11.3
  • Fasta index is created if non-existent
  • Candidates.txt shows PASS or fail reasons
STAR-SEQRv0.3.0:
  • Big release!
  • Better modularity in code
  • Speed improvements for all annotation functions
  • Improved logging
  • Fixed a bug in bed subsetting when using the "both" style
  • No longer produces the same style of bedpe/VCF for Fusions.
  • New Fusion bedpe using proper coordinates
  • Support fastqs are broken into more coherent groupings: span, split, overhang
  • Cross homology checks now use span and overhang reads separately
  • Fixed a primer bug where breakpoints were not being used correctly in some cases
  • Fixed several bugs that were introduced that prevented DNA mode from working.
STAR-SEQRv0.3.1:
  • Fixed install script and now use sdist and twine for Pypi uploads.
STAR-SEQRv0.4.0:
  • Updates to STAR functions to use the new chimMainSegmentMultNmax parameter.
  • Allow more ways to run STAR-SEQR from different STAR outputs.
  • Salmon is now used to quantify candidate fusions and partner transcripts.
  • Additional parameter (-x) to pass in a transcript reference for more stable counts.
  • Greater sensitivity. Now rescues reads with 1 read support as long as all other filters and expression metrics are met.
  • Uses more filtering approaches including basequalities, expression of transcripts relative to fusion,
  • Fixed a bug so fusion junctions are now normalized to 0-base genomic coordinates.
STAR-SEQRv0.5.0:
  • Creates a central folder "chimeric_transcripts" for all fasta files.
  • Functions now pull fastas from central chimeric transcript folder
  • Reference transcripts are now extracted directly from the GTF. The (-x) parameter is no longer in use.
  • Multimapping homologous fusions are considered through a network graph approach where homology and expression are used to prune clusters. If homologous the highest expressing homolog passes the filter. If they share a breakpoint but are not considered homologoues, then all partners pass the filter.
  • The highest expressing fusion transcript is now part of the output
  • Primers are now generated from the highest expressing transcript.
STAR-SEQRv0.5.1:
  • Added bioconda recipe
  • Updated basespace script
  • Modified threshold for num of jxns to minfrag20 ratio from 10% to 1%. This filter was removing TPs in some datasets and other filters are catching FPs in our training datasets.
STAR-SEQRv0.6.0:
  • With a compendia of training data tweaked thresholds to keep FP from exploding in especially noisy samples such as FFPE.
  • Added more info columns to the output
STAR-SEQRv0.6.1:
  • Fixed a bug where fastq input was marked required but would break when run using existing alignments
  • Added cwl for starseqr
STAR-SEQRv0.6.2:
  • Changed map multiprocessing to map_async which leads to overall better performance
  • Filters mitochondria junctions earlier in the process which also imporoves performance
  • symlink gtf into folder and make table locally rather than externally. Helpful for CWL
  • changed memory to low requirement for pandas read_csv to avoid segfaults on large inputs
  • use salmon "A" library type
STAR-SEQRv0.6.3:
  • fixed a filtering step that would die if all junctions were based on previous filtering
STAR-SEQRv0.6.4:
  • Allow prefix to be a string or a full path. Helpful for writing outside of current working directory.
  • Removed DNA functions as this has been deprecated for some time.
STAR-SEQRv0.6.5:
  • Primer generation step was taking too long. Modified to search only 200bp on each side of breakpoint.
STAR-SEQRv0.6.6:
  • If no fusion transcript is identified skip primer generation. This was causing errors in some systems.
STAR-SEQRv0.6.7:
  • General code cleanup and catches for some edge case scenarios.