v1.1

• -psi, -flatten added for PISA anno;
• Add new tools gtf2bed and flatten

v1.0 pre-release

• New (expressed peak tag) EPT calling method added.
• annobed and mergebed methods added.
• New parameters added to anno , see usage for details.

v0.12: modified: PISA_manual.pdf

1. PISA count supports multithreads
2. PISA count supports BAM with spatial coordinates
3. PISA anno supports a new alignment type, antisense intron

v0.12b

• New designed parse tool, PISA parse2, now is released.
• Accepts unsorted GTF.

v0.10

• Support export spliced and unspliced matrix for velocity analysis
• Update bam2frag to export to fragments file

v0.9

*Rewrite rmdup

v0.8

1. reduce memory usage of count
2. fix bed query bug of anno -bed
3. add anno -vcf method

v0.7

qual

v0.3: modified: README.md

	modified:   src/main.c
	modified:   src/sim_search.c