CHANGELOG

Version 1.1.5 (1/20/16)  - added TPM and ECPM estimates for genes and isoforms
			 - added option to compute confidence intervals (bootstrapping)
                         - added option for reading alignments from standard input

Version 1.1.4 (12/31/15) - added `endseq` option

Version 1.1.3 (10/11/15) - bug fix in handling CIGAR with indels in convert-iso-to-genome-coords
			 - bug fix related to hisat/hisat2 alignments

Version 1.1.1 (11/5/12)  - bug fix related to clipped read alignments (CIGAR with S field)

Version 1.1.0 (4/24/12)  - added support for alignments with insertions and deletions

Version 1.0.6 (8/12/11)  - extract-isoform-sequences-from-genome (see 
			   http://dna.engr.uconn.edu/software/IsoEM/README-SAMPLE.TXT)
			   generates transcripts in a randomized order
			 - isoviz generates a gtf with fpkm values
			 - added output file name option

Version 1.0.5 (5/08/11)  - bugfix related to paired read data

Version 1.0.4 (2/22/11)  - added polyATail option
                         - further memory and speed improvements

Version 1.0.3 (8/30/10)  - correct for annotated repeats

Version 1.0.2 (8/05/10)  - improved memory requirements for storing genome sequence
                         - added hexamer bias correction option
                         - added isoviz visualization tool

Version 1.0.1 (6/25/10)  - added support for mate pairs
                         - added support for max number of mismatches
                         - performance improvements

Version 1.0.0 (6/16/10)  - first public release