Chaining script improvements: 5 merge, output fasta/fastq

[Magdoll]

Improvements to chain_samples.py

Top priority:

• allow 5' merge, that is, if one isoform in sample A is a 5' truncted form of another in sample B, allow them to be chained as equivalent and select the longer form. Prerequisite: both sample A and B must have already gone through collapse using 5merge option, otherwise results can be incorrect.

• output fasta/fastq files along with the current output of chained GFF, ids txt, and count.

Medium priority:

• allow iterative chaining via pickled object

[Magdoll]

5merge is now allowed via chain_samples.py --allow_5merge
fastq output is now supported via sample.config having an optional FASTQ_FILENAME=xxxx.

code updated to version 2.4.

tutorial available here