Skip to content

Major Release v1.0.1
Compare
Choose a tag to compare
@maschon0 maschon0 released this 03 May 09:49
· 26 commits to master since this release
v1.0.1
cfd6dbe

Bookend Release Version 1.0.1

A number of behavioral changes, bugfixes, and new utilities are introduced in this new major release. See the new v1.0.1 Bookend User Guide for current utility usage and arguments.

Behavioral changes:

  • All utilities can now stream data directly from gzipped input file(s).
  • For all utilities, all argument defaults are now displayed in the --help text.
  • bookend elr no longer writes unsorted ELR files; default ELR output will always be position-sorted.
  • bookend elr identifies additional end tags through softclipped alignments that were too short to be called by bookend label.
  • Column 7 of an ELR file may now contain a triple of scores so that the number of start/end tags is not lost during condensed assembly (formatted as three floats between pipe symbols, cov|start|end).
  • bookend label reverses all reads of an input FASTQ file if using the argument --strand reverse.
  • bookend assemble no longer uses source information by default; use argument --use_sources to enable.
  • bookend assemble GTF output attributes "S.reads", "S.capped", and "E.reads" now contain the proportional weight of the tag clusters assigned to that isoform, rather than the full weight of the tag cluster.
  • bookend assemble pre-filters branchpoints from the Membership Matrix if an adjacent gap in read coverage would prevent them from being in a complete path.

New utilities:

  • bookend bedgraph writes Bedgraph-format files of read coverage or tag abundance by genomic position.
  • bookend fasta takes an annotation file (GTF/GFF3/BED12) and a genome FASTA, and writes a transcript-level FASTA file.
  • bookend gtf-ends writes a BED file of the unique set of 5' or 3' clusters represented in an annotation (GTF/GFF3/BED12).

Bugfixes:

  • Prevented dropping the last temporary block of reads during bookend elr-sort.
  • In bookend assemble, corrected the Overlap Matrix decision tree to allow for mutual containment.
  • bookend assemble no longer terminates new path construction at a locus if a new path gets trimmed to match an existing path.
  • Prevented duplicate ELR headers in output of bookend elr-combine.
  • bookend condense no longer skips chunks of length 1
  • FASTA utilities used the wrong complement to the IUPAC ambiguity code "R".
  • Prevented malformed transcript ends from being introduced during bookend assemble by get_transcript_attributes
Assets 2
Loading