Outline script
Add sample bam file for testing
Add sample FASTA reference file for testing
Add expected FASTA output file for testing
Test extraction: 10bp upstream of reads (P:0/1)
Get options from CLI
Parse bam file
Get read info
Add scaffolds for subs extract_flanking_seqs & write_to_fasta
Get start/end positions for FWD strand seqs
Get start/end positions for REV strand seqs
Extract flanking sequences
Write to fasta
Sort output and fix order of expected.fa for testing (P:0/1)
Fix typo in expected FASTA sequence (P:1/1)
Sort read IDs by coordinates before writing FASTA
Fix sorting
Fix order of expected FASTA sequence (P:1/1)
Update expected FASTA file to allow duplicate read IDs
Allow duplicate read IDs (caused by paired mates)