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0.4.29

  • Update handling of --database argument #90

0.4.28

  • fix random order in Variant field #84

0.4.27

  • fix possible duplication of lines #80
  • accept prefix for gff output #84

0.4.26

  • Support spaces and special characters in bam files

0.4.25

  • fix outliers samples. When there is no identification of reference sequences or isomirs, the multiqc module will fails because it won't find the expected keys. Adding 0 when is the case.

0.4.24

  • fix bad annotation when 5 or more T/A at the end of the sequence by @DrHogart
  • Add SQL database creation

0.4.23

  • fix empty stats file #61 by @leontienvdbent

0.4.22

  • fix when reads map halfway on to the edge
  • fix edge case where limit==variant_size

0.4.21

  • Missing trimming events since 0.4.19

0.4.20

  • Support export isomiR rawData output
  • Support genomic coordinates as output in the gff
  • Make TOOLS mandatory in header
  • Implement method to create gff line
  • Improve docs

0.4.19

  • Add --version option
  • Fix bug that ignore sequences starting at 0 in bam files

0.4.18

  • Cast map object to list to avoid errors in py3.
  • Support Manatee output.
  • Support chunk reading for genomic BAM files.
  • Support chunk reading for seqbuster files.
  • Support chunk reading for BAM files.
  • Normalize functions to support different databases.
  • Support miRgeneDB.
  • Export to VCF. Thanks to Roderic Espin.
  • Support isomiRs that go beyond 5p end
  • Support genomic coordinates.
  • Fix missing reads when using --keep-read in the final mirtop.gff file.
  • Allow longer truncation and addition events.
  • Accept seqbuster input without frequency column.
  • Allow keep name of the sequence.
  • Accept indels in snv category.
  • Additions are only last nucleotides that are mismatches.
  • Adapt mintplate license.
  • Revert sign in iso_5p, replace snp by snv.
  • Skip lines that contain malformed UID.
  • Add FASTA as an exporter from GFF.
  • Fix BAM parsing to new GFF rules.
  • Add the possibility to work with spikeins to detect random variability.
  • Fixing UID attribute for tools that don't use our cypher system
  • Add class to parse GFF line as a first move toward isolation
  • Add JSON log for stats command.

0.3.17

  • Normalize the read of the tool outputs.
  • Add docs with autodoc plugin.
  • Validator by @Vbarrera.
  • Improve examples commands and test coverage.
  • Only counts sequences with Filter == Pass during stats.
  • Counts cmd add nucleotide information when --add-extra option is on.
  • Fix error in stats that open the file in addition mode.
  • Importer for sRNAbench just convert lines from input to GFF format.
  • Skip lines with non-valid UID or miRNAs not in reference at counts cmd.
  • Fix separators in counts cmd.
  • Make --sps optional.
  • Add synthetic data with known isomiRs to data set.
  • Allow extra columns when converting to counts TSV file.
  • Allow extra attributes for isomir-sea as well.
  • Allow extra attributes to show the nts that change in each isomiR type.
  • Fix Expression attrb when join gff files.Thanks @AlisR.
  • Print help when no files are giving to any subcommand.
  • Fix bug for duplicated isomiRs tags. Thanks @AlisR.
  • Fix bug in order of merged gff file. Thanks @AlisR.
  • Add module to read GFF/GTF line in body.py
  • Add version line to stats output
  • Improve PROST! importer
  • Fix output for isomiRs package

0.2.*

  • Make GTF default output
  • Add function to get SNPs from Variant attribute
  • Improve PROST with last version output
  • Add isomiR-SEA compatibility
  • Fix sRNAbench exact match to NA in GFF
  • Change stats to use only 1 level isomiR classification
  • Add GFF to count matrix
  • Add read_attributes function
  • Improve isomiR reading from srnabench tool
  • Add PROST to supported tools

0.1.7

0.1.5

  • add function to check correct annotation
  • add test data for SAM parsing
  • add script to simulate isomiRs
  • parse indels from bam file

0.1.4

  • fix index BAM file command line
  • add function to accept indels and test unit
  • change header from subs -> mism to be compatible with isomiRs