Overrided z-score function added.
AddEndRNASeqToScripture adds end RNA-Seq information to reconstructions/
any annotation file.
GeneWithIsoforms.setBedScore(double) was corrected. Was giving an error
earlier.
rap classes were modified to add the "All" score, which outputs 3
scores: log2ratio, binomial p-value & skellam
Major changes to the Alignment classes:
* Each alignment object does not have its own transcription read object,
instead that argument is used in the constructor to set the orientation
of the paired end alignment. Single end alignments were setting their
orientation in the PairedEndWriter based on the transcription strand.
* PairedEndAlignmentFactory will be used to determine which paired end
alignment is returned by the PairedEndReader.samRecordToAlignment()
* Default paired end alignment is fragment and TranscriptionRead.UNKNOWN
* Correction to instantiation of FragmentAlignment now sets the name of
the alignment.
Bug fixed in Gene class:
When instantiating a Gene object from a Bed entry the bed score was not
being set. Corrected now.

AnnotationCollection returns the ReferenceLambda.

TODO: AnnotationList returns 0 as lambda
GenomicSpace.getUnmaskedLength() added

TranscriptomeSpace.getWindowIterator(Collection<Gene>) throws an
IncompleteMethodImplementationException instead of simple returning
null.
Major change:
AlignmentModel & PairedEndReader changed to account for the use of
PairedEndAlignmentFactory. And the TranscriptionRead is now an attribute
of the PairedEndReader class, which is instantiated from the
Alignmentmodel.
rap.WindowAllScore added
Major changes to Scripture.

Now uses stranded information, uses the boundary 1bp regions to check
for all drops in coverage drops.

EndPileUpScanner can be used to annotate annotation sets using end
RNA-Seq data.

Assembly has a confidence flag.
PairedEndWriter also supports the TranscriptionRead for stranded data.
PairedEndAlignmentTest is used to test a test bam file with different
combinations of TranscriptionRead and fragment boolean
SameOrientationFilter added to check whether the read has the same
orientation as a passed Annotation object.
Merge remote-tracking branch 'origin/master' into scripture-pairedRead

Conflicts:
	src/java/nextgen/core/writers/PairedEndWriter.java
Latest sam jar file added by Manuel, re-added for Egit
No change commit. xml files in the parent
Merge remote-tracking branch 'origin/master' into scripture-pairedRead

Conflicts:
	bin/nextgen/core/programs/MarkDuplicatesFromNameUMI.class
	src/java/broad/pda/annotation/BEDFileParser.java
	src/java/nextgen/core/alignment/FragmentAlignment.java
	src/java/nextgen/core/alignment/PairedReadAlignment.java
	src/java/nextgen/core/annotation/Gene.java
Merging