Stictching algorithm

[joshfactorial]

Given a set of runs from files generated in the previous example: stitch files back together, so at the end we have a single fastq (or two for paired ended), a single golden bam and a single golden vcf covering the entire orginal fasta file.

Given an input of 2 or more output files from split runs, and the original NEAT read-simulator configuration file, reconstruct the output into a single set of files.

• Combine fastqs by lane, keeping paired ended reads in tact
• Combine smaller bams into one
• Combine smaller vcfs into one
• All files should be valid and have appropriate headers (as best we can)

NOTES: there was a script in NEAT 2.0 that did this, so that would be a good place to start.