-
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: #47 bcbio/bcbio-nextgen#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