This release includes the following updates:
- Some aligners such as ELAND do include the MQ tag in their alignments. For now, in such cases indelMINER assumes that the mapping quality of the mate sequence is the same as the mapping quality of the sequence.
- samtools version 0.1.19 is included with this code, so it can be built independently.
- Introduced another option "-b" to indelMINER, which forces it to require at least one read with these number of bases on both sides of the indel. By default at least one read that has 30 bases on either side is required.
- Supplementary alignments are now ignored in the analysis of the pairs.
- The VCF output should now work properly with IGV.
- Changes to the test cases and README.