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

v0.2.11

• 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
• Remove deletion from addition isomiRs
• Support for srnabench output
• Fix bug mixing up source column
• Support Seqbuster output
• Functin to guess database used from GTF file through --mirna parameter
• Adapt output format to https://github.com/miRTop/incubator/blob/master/format/definition.md
• add function to check correct annotation
• add test data for SAM parsing
• add script to simulate isomiRs
• parse indels from bam file
• fix index BAM file command line
• add function to accept indels and test unit
• change header from subs -> mism to be compatible with isomiRs