v1.3.4

• updates to Makefile
• updates to code for compatibility with new gcc version
• linked read analysis using MI tags

v1.3.1

• fixes compiler warnings
• some bug fixes
• fixes prune_haplotype.py to output valid file

1ee1d58

minor update

v1.3

This release:

1. Uses fast logsum approximation for likelihood calculations that speeds up HapCUT2 by 7-8 times
2. updates extracthairs for PacBio CCS/HiFi reads
3. includes several bug fixes and reorganization of the code

v1.2

This release updates the htslib API calls, allowing extractHAIRs to be compiled with recent versions of htslib.

v1.1

This is a new release of HapCUT2 that fixes bugs and significantly improves the allelotyping for long SMS reads.
Use the following commands to download and compile this version:

git clone --recursive https://github.com/vibansal/hapcut2
cd hapcut2
git checkout 3cb79c1
make

v1.0

This is a release of the current version of HapCUT2, a haplotype assembly tool for diploid genomes using high-throughput sequence data. This is a stable version. Use the following commands to download and compile this version:

git clone --recursive https://github.com/vibansal/hapcut2
cd hapcut2
git checkout 467734a
make