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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

  • 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