Changes v1.4

1. Optimize the determination of stitching in "auto" mode
2. Change the distance to call self-circles to 10
3. Fix a bug in reporting self-circle numbers
4. Add a script to remove unplaced contigs in reference genome
5. Update Ktrim to v1.6

changes in v1.3

1. Optimization on index file structure
2. Bug fixes in "build.index.sh" and "run.example.sh"
3. Discard the "splice-awareness mode"
4. Add more detailed information in README

Major changes in v1.2:

1. Change the default aligner to BWA
2. Add option "-e" to set minimum mapping integrity
3. Add option "-Q" to set minimum mapping score
4. Pipe preprocessing procedures

Changes in v1.1.1:

1. Add the scripts used in benchmark evaluations (under benchmarking/ directory)
2. Add "-N" option to disable STAR's splice-awareness mapping
3. Bug fixes.

Changes in v1.1.0

1. Provide a utility to add genomes
2. Provide a utility to analyze EBV-related loops
3. Pipe Ktrim, Krmdup, and FLASH for higher speed
4. Pipe samtools and sam2pairs
5. Set "scoreGapNoncan -4" for STAR

First public release of Microcket.

Major features:

1. Extra-fast
2. Higher sensitivity (i.e., report more interactions)
3. Optimized alignment strategy for emerging Micro-C protocols
4. Data preprocessing and multi-step quality controls
5. Built-in support for multi-files and biological replicates