Post-alignment processing

[averagehat]

After discussion with @InaMBerry, some of the below might be possible:

• Marking Primer-induced errors
  • This would require parsing the trim_stats files in order to know how much of the primer was already trimmed; A primer file could also be involved
• marking pcr duplicates
  • picard has a "markDuplicates" command-line function
• marking gaps in alignment
• stop codon where it shouldn't be
• indel detection (picard indelReAligner)

[averagehat]

related to #149

[averagehat]

This may be better off in the bio_bits project. sort of like: https://github.com/VDBWRAIR/bio_bits/milestones/Analyze%20Alignments

[necrolyte2]

Yes, have it in bio_bits then just include here and use