umi error fixed

Avoid error when read name contains ILLUMINA word

v.1.2.8

Fix bug when detecting the end of the cluster due to big gaps in biopython function

v1.2.7

• Fix bug when writing files for debug of big meta-clusters:
  #47
  bcbio/bcbio-nextgen#2948
• Add version option

v1.2.5

• Fix error when the precursor is too long to ignore RNAfold calculation. Thanks to @ZhuZhuoHSPH and @kthlnktng

v1.2.4

• 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.

v1.2.4a3

• Support UMI tag when collapsing
• Add count matrix for each sequence

v1.2.3

• 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

Improve bedtools usage

• 1.2.2
  • Use bedtools for bamtobed and clustering
  • Only update seqcluster code when upgrading
  • Add beter logging to prepare sub-command

seqcluster-v1.2.1

• 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