script to parse SL3.0 chrs using SL2.93 TPF files and extract contigs

[suryasaha]

Compare list of gap sizes from SL2.93 TPF file to stretches of N's in chr to identify start/stop coordinates.

Account for contamination fixes

• chloroplast contamination https://github.com/solgenomics/data/issues/60
• arabidopsis contamination https://github.com/solgenomics/data/issues/22

Output

• Fasta of contigs
• TPF with temp contig names and correct gap sizes