Mirtop

* 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.

* 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

* 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