getMates() function added to Alignment classes
Conflicts merged and Gene.getFirstIntron() function is added.
Major changes to ESAT:
1. Bug in opposite strand fixed.
2. Step size reduced to 20
3. Collapsing genes is more accurate
4. Output files have changed to include collapsed.additiveIsoforms,
collapsed.bestIsoform and fullgene.matrix now only adds signal from
significantly expressed windows.
5. All significant windows are output
6. debugMode has been added
globalPairedEndFragments removed from global stats file. globalCount
calculation is improved. Redundancy removed.
Minor change
FastqConsolidateBarcode is added to add the molecular barcode to the
read name. Paired end and single end support.
EndSeq made faster.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git