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- 1.2.9
* Fix bug where UMI is mistakenly detected in read names containing "ILLUMINA"
- 1.2.8
* Fix bug when detecting the end of the cluster due to big gaps in biopython function
- 1.2.7
* Fix bug when writing files for debug of big meta-clusters:
https://github.com/lpantano/seqcluster/issues/47
https://github.com/bcbio/bcbio-nextgen/issues/2948
* Add version option
- 1.2.5
* Fix error when the precursor is too long to ignore RNAfold calculation. Thanks to @ZhuZhuoHSPH and @kthlnktng
- 1.2.4
* Fix multiple errors when running in python 3 due to map function.
* Fix error in collapsing fasta files.
* Fix end of line character for counts_sequence.tsv.
* Remove `map` function from quality class in collapse function to avoid seg.fault in python3.
* Use DESeq2 normalization strategy.
* Fix more errors in python3 env.
* Fix UMI checking when the input file is a gzip file. Thanks to @rbatorsky-claritas.
* Fix header bug
* Initiate migration to py3*. Thanks to @smoe.
* Include mirtop annotation.
* Fix upgrade command.
* Fix UMIs detection to count using unique seq + umi. Thanks to @mshadbolt
* Remove Cpy code and use biopython
* Clean test examples
* Fix UMI error when sequences have different sizes. Thanks to @mshadbolt
* Support UMI tag when collapsing
* Add count matrix for each sequence
* Remove HTML report
* Allow size parameter during collapsing reads
* Fix reporting DB when precursor is masked
* Add conflict to output
* Fix bug in prepare sample that will setup min-shared
to samples size always.
- 1.2.3
* Add --feature_id as an option to specify the attribute
to use in the GTF file for annotation
* Add gene_id as a 2nd option to add GTF annotation
* Only do rnafold for precursors shorter than 200nt
- 1.2.2
* Use bedtools for bamtobed and clustering
* Only update seqcluster code when upgrading
* Add beter logging to prepare sub-command
- 1.2.1
* Fix expression profile when no sequence at that position
* Fix reading from profile file to avoid calculation
- 1.2.0
* Add function to map SNPs to genome coordinate
* Add RNAfold to report for html vis.
* Adapt C code to macosx
* Improve test functions
- 1.1.14
* Improve miRNA annotation function and add first functions
to allow SNP detections
* remove bcbio funtions to simpler to avoid circular dependency
* add function to get targets from targetscan for human
* select best precursor based on size
* parse pyMAtch to be compatible with other tools
* add C function working as miraligner by @franpantano (pyMatch)
- 1.1.11
* first version of simulator of 33 nt long sRNA from fasta
* add Rmd template for bcbio pipeline
* add peak detection to cluster, as a try to get the mature sequence
- 1.1.8
* fix indexing bam file error when running under python
* remove colorlog dependency
* create light package in conda for bcbio installation
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