- Fix problem with building indexes with more than 8Gbp of reference sequence.
- Add option to append text to every read header in SAM and Native report formats. -o Header text will append text to every read header. Some users requested this to add slide/lane data to read headers in colour space.
- For Bisulphite alignments change default homopolymer filter setting to 120 (i.e. default is -h 120)
- Fix: When -K Filename was being used to write quality calibration file the calibration data for read 2 of pairs was incorrect.
- Fix a Seg Fault that could occur if read lengths were less than the index k-mer size. Short reads resulted from trimming adapter sequences.
- Fix interpretation of mpileup base qualities when base string contains a $. This had caused bases and qualities to become misaligned. Novomethyl should probably be rerun to correct results.
- Add capability to convert Bi-Seq alignments.
Release Novoalign V2.07.08 & NovoalignCS V1.01.08
- Fix for single end conversion, previously was setting paired end flags.
- Fix Assertion failed: (tgttposn != '\0') which could occur if read aligned at the end of a reference sequence.