Fixed the SlideAndCalculate class. Works with bedgraph files now. TODO:
Check why bed files fail.
Fixed a bug in calculation. Will calculate scores for all windows, not
entire chromosomes.
Fixed a bug introduced by my earlier revision, so that if a Gene does
not have a name, it will not exit (reverted)
PairedEndReader modified to allow handling of non-paired end bam files -
the original files. Earlier, the single end alignment objects formed
from paired end reads were not oriented by the transcription strand.
Bug in CanonicalSpliceFilter is fixed. If a genome sequence is not
provided, all "spliced" reads will return true. Bug was that all reads
returned true.
Major changes to Scripture, especially initial assemblies.
Multiple classes added for processing of reconstructions. TODO: Merge
the classes into modular architecture called from one main class.
Some debugging statements added to PairedEndWriter
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git