whats new:

1. improve the performance on re-identification and quantification for isoforms
2. check the TSS and TES of queried transcirpts by default
3. reduce mem usage
4. code clean
5. Changed positive samples and dected column in isoform output. the foramt now is fsm+em:fsm:em

whats new:

1. new function for fusion query is available for querying two regions instead of two breakpoints.
2. small tweaks

small tweaks

bug fix:

1. fix panic when missing chromsomes in tree for mono-exon search

bug fix:

1. add missed format string for each output line in isoform output.

whats new:

1. new quantifiaction method based on EM algorithms
2. smaller index size(30% reduction)
3. better identification on mono-exons
4. optimization on runtime and memory usage

improvements:

1. fix the OOM when a trascript has huge number of reads(e.g., transcripts in chrM).

improvement:

1. reduce the memory usage a little bit.

whats new:

1. assemble mode is available. it uses fragmented reads for identification and quantification. it can be enabled with --asm
2. extremely reduce the memory usage for querying isoform.