v1.3

Major change

This version mainly improved the phasing accuracy, especially at low-coverage depth (10-20x). The underlying graph model now creates and considers multiple edges from local/flanking SNPs during phasing (see below), which increases the phasing accuracy and robustness at regions of dense ONT errors.

As such the running time increases ~20% on average (2.5-8 minutes for 10-60x with 8 Cores on SSD). The block N50 becomes larger at 10-30x and slightly smaller at 50-60x when compared with previous version. The phasing accuracy (SW: switch error rate) improved at all coverage.

Minor change

1. The haplolag now writes the Phred-scaled phasing quality of each read in the tagged BAM (e.g., PQ:i:40), which was discussed at #19.

2. The program will prompt the user if missing the reference genome. #18