v0.4.28

Fix issue 83 with random order of Variant field

v0.4.27

• Fix duplication in counts file
• Fix randomness order in GFF Variant attribute
• Add option to control file output name

v0.4.25

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.

v0.4.24

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

v0.4.23

fix empty stats file #61 by @leontienvdbent

v0.4.22

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

v0.4.21

• Fix missing trimming events since 0.4.19

v0.4.20

• 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

v0.4.19

• 0.4.19

• Add --version option
• Fix bug that ignores 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.

v0.3.17

• 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