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Release Novoalign V2.07.09 & NovoalignCS V1.01.09

Posted by colin on Tue 08 of Mar., 2011 11:49 MYT

novoindex

Fix problem with building indexes with more than 8Gbp of reference sequence.

novoalign*

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)

novoalignMPI

Fix: When -K Filename was being used to write quality calibration file the calibration data for read 2 of pairs was incorrect.

novoalignCS

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.

novomethyl

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.

novo2sam.pl

Add capability to convert Bi-Seq alignments.

Release Novoalign V2.07.08 & NovoalignCS V1.01.08

novo2sam.pl

Fix for single end conversion, previously was setting paired end flags.

novoalignCS

Fix Assertion failed: (tgttposn != '\0') which could occur if read aligned at the end of a reference sequence.

Reads: 4203

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