enable PAMI support by default

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
print large contig names for debugging

Link: https://github.com/GeneAssembly/biosal/issues/659
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
implement STATUS_DISAGREEMENT in unitig walker

[boisvert@bigmem biosal]$ ./scripts/assembly_debugging/check-names.sh 1.fasta
Got names
Got defect names
Check DefectList.txt (defects: 0 / 1663)
4 longest:
19220
17580
16515
16300

Link: https://github.com/GeneAssembly/biosal/issues/653
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
isolate code that checks symmetry

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
isolate code that check agreement

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
isolate code that checks usage

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>