v1.3

New or improved features

• Support reads containing indels (closes #25 and #45).
• Refined process for dealing with overlapping reads (closes #15).
• Improved documentation (closes #82 and #84).
• Python 3.4 support.

Minor improvements

• Added NEWS file.

Bug fixes

• Provide default --ir1p and --ir2p (closes #79).
• Switched to *nix style line endings (\n), rather than the Windows line endings (\r\n), for the .tsv file (closes #83).
• Switched back to samtools instead of Picard in helper_scipts/run_comethylation.sh (closes #78).
• Updated examples to use Bismark v0.12.5.

Internal

• Simplified creation of m-tuples.
• Added get_positions function to get the reference positions of all bases in a read (including None if no reference base, such as inserted bases or soft-clipped read-positions).
• Added process_overlap function to process overlapping paired-end reads using the given --overlap-check

:(

• Running time of v1.3 is 2-3x slower than v1.2. Partly because reads with indels are no longer skipped and partly because of code simplifications. Should be able to improve performance now that some internals have been simplified.