-
Added Hi-C functionality using the option
--hic. This expects data in the format output by HiCUP, so a paired-end data format, where read-pairs follow each other on consecutive lines. Deduplication occurs on mapping combinations where read pais can be mapped as either R1/R2 or R2/R1. All modes of deduplication work, i.e. just positional, UMI (no mismatches), or UMI with mismatches. -
Added a detailed UMI report for Hi-C mode, using the option
--detail. This outputs a file in the following format:
UMI count R1 chrom R1 pos R2 chrom R2 pos
TAAAGCGATCT 116 chr17 65539294 chr17 65540317
- Changed auto-detection to identify single-/paired-end for Bowtie2, HISAT2 or Bismark, and just once per @PG line.
- Added handling of softclipped reads (CIGAR operation: S)