Ribotish

Tisdiff bug fix

Update log factorial calculation

Lower the threshold between fasttest and normal test to increase testing speed.

Some python3 compatibility updates.

Update codes to allow genes with transcripts in different strands in chromosome.

Add --blocks option to report all exon block positions for predicted ORFs.

Change chisqprob to chi2.sf since chisqprob was deprecated in newer versions of scipy.

Update NegBinom test pvalue function, more accurate and faster.

Update GTF attribute extracting function.

Update tisdiff R scrpts to allow non tab seperators.

Update docs, especially for python3. Ribo-TISH codes are compatible with both python2.7 and python3.

Add --colorblind option in quality to generate another color style readable for color blind people.

Add --colors option for customizing color style.

Some doc updates.

Many updates.

Add TIS initiation efficiency comparison in tisdiff.

For replicate data, tisdiff still cannot deal with replicate samples, but can now export count table for replicate samples.

Add '--chrmap' option to match different chr name versions between fasta, bam and gene annotation files. Simple conversions such as 'chr1' to '1' will be matched automatically without using this option.

Quality can print total effective RPF counts that were assigned offset values in annotated CDS regions under -v option.

Add R scripts for differential TIS with replicates.

Add --allresult option for saving non-filtered results.

Fisher's method p-value will report None for regular Riboseq only prediction.