Hit.mismatches doesn't account for indel length

[nh13]

I think we count a multi-base indel only once when subtracting the indels from the edits to obtain mismatches
https://github.com/fulcrumgenomics/fgprimer/blob/6cf2542e927ced37dd0dce4c335de8dff07789c7/src/main/scala/com/fulcrumgenomics/primerdesign/offtarget/BwaAlnInteractive.scala#L94C7-L94C12

@tfenne thoughts?

[nh13]

Check out these test cases:

1. the first query (q1) exactly matches the reference, and the NM tag has value zero.
2. the second query (q2) has one 2bp deletion and a single mismatch and the NM has value three, which would set Hit to have edits to three, so then the mismatches method would return two instead of the expected one.

test.fq

@q1
AGTGATGCTAAGGGTCAAATAAGTCACCAGCAAATACACAGCACACATCTCATGATGTGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@q2
AGTGATGCTAAGGGTCAAATAAGgCACCAGCAAATACACCACACATCTCATGATGTGC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

test.sam

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:chr1	LN:10001
@PG	ID:bwa	PN:bwa	VN:0.7.17-r1198-dirty	CL:bwa aln -S tests/offtarget/data/miniref.fa test.fq
q1	0	chr1	1081	37	60M	*	0	0	AGTGATGCTAAGGGTCAAATAAGTCACCAGCAAATACACAGCACACATCTCATGATGTGC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:60	HN:i:1
q2	0	chr1	1081	37	39M2D19M	*	0	0	AGTGATGCTAAGGGTCAAATAAGGCACCAGCAAATACACCACACATCTCATGATGTGC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:2	MD:Z:23T15^AG19	HN:i:1

miniref.fa

>chr1
CAGGTGGATCATGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAGCCCCACC
TCTACTAAAAATACAAAAAATTAGCTGGGCATGATGGCATGCACCTGTAATCCCGCTACT
TGTGAGGCTGAAGCAGGAGAATTGCTTGAACCCAGAAGGTGGAGGTTGCAGTGAGCCGAG
ATTGCGCCATTGCACTCTAGCCAGGGAGACAAAGCAAGACTCCATCTTGAAAAAAAATAA
TTAAGCTAGCAGACTGGGCAGGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCCGA
GGTGGGTGGATCACCTGAAGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAATAC
CCCATCTCTACTAAAAGTACAAAAATTAGCTAGGCATGGTGGCTCATGCCTGTAGTCCCA
GCTAATTGGGAGGCTGAGGCACGAGAATCGCTTGAACCTGAGAGGTGGAGGTTGCAGTGA
GCCCAGATCACGACACTGCACTCTAGCCTGGGCAACAGCATGAGACTTGGTCTCAAAAAA
AATAAGTCAATAAGACAAAAAAAAAAATTCAGCTAGCAATCTTGAATTTTACTGATTTAC
TTGAATATATAATTAACTTTAAATTTATATGCTTGTTCATGTACATGTAAGGAAAATACA
TTCCATAAAAAATCACAGATATAGTACTTAGATCTTTAAACTGTAGGGTCTAGGAAAATA
ATAAATGATCGCCTCTTTTTTTGTTGTTGTTGTTGAGATGGAGTCTCTCTCTGTTGCCCA
GGCTAGAGTGCAGTGGTGCGATCTCGGCTCACTGCAACCTCTGCCTCCTGAGTTCAAGCA
ATTCTCCTGCTTCAGCCTCCTGAGTAGCTGGTATTACAGGTGCCCACCACCTCTCCTGGC
TAATTTTTGTATTTTTAATAGAGACGGAGTTTTACCATCTTGGCCAGGCTGGTCTTGAAC
TCCTGACCTCGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGC
TACCGTGCCTGGCTGATTGCCTCTTTTTTAGTAGTAGAAGTGAGGTAAATGCCTGTTGGC
AGTGATGCTAAGGGTCAAATAAGTCACCAGCAAATACACAGCACACATCTCATGATGTGC
TCCAGCTGGCATCTCATTTGAGGGCAGAAAATCACTCCCTTTTGTCTAAAAACTAGTGTT
CAGGAACTGATCCTGCAGCTCCCACCCGGGCTCTGGCATCACTCTCTCCCAGCATTTGCC
AAACCGCAGTGAGAAGAAAGGCAGCTTGTCTTTGCACAAAGAAGCAAGTTTACTTGGGTT
TTTTGAGATAGGGTCTTGCTCTGTCGCTCAGGCTGTAGTGCAGTGGTGCGATCATGGCTC
ACTGCAGCCTTCACTTCCTGGGCTCAGGCGATCCTCCCACCTCAGCCTTCCAAGTAGCTG
GGACAACAGGTGCATACCACCACACTTGGCCAATTTTTCAATTTTTTTGTAGAGACGGTG
TCTTGCTGTGTTGTCCAGGCTGGTCTCAAACTCCTGGCCACATGCAATCCTCCTGCCTCT
GCCTTGCTTGGGTTTTAATATTTGGAGCTAACCTGGGATTTGGGAGTTCCTGGTGTACCC
CCACAGCAGCCAAGGACACTGAAGGTGCGTGCTTCAGAAATGGAGAAGCCCCATGTTAAT
GCCCACAGATATTGACTAACTTGTGCAAGTCCTCGCCTTTAGTCCTGTTATGAACCCAAG
AAGGTGGTGGTGTTACTAACTTGTCCCAGATTACTGTGTACACTGGGATATATTTATTTA
ATTTAATTAGTTTATTTATTTATTTATTTATTTATTTATTTATTTTTGAGACAGAGTCTC
CCTTTGTTGCCCAGTCTGGAGTGCAGTGGCACGGATCTTGGCTCACTGCAACTCCGTCTC
CCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCACACGC
CCCCACACCCCGTTAATTTTATATTTTTAGTACAGACAGGGTTTCACCACGTTGGCCAGG
CTGGTCTCGAACTCCTGAGCTCAGGTGACCTGCCTGCCTCGGCCTCCTAAAGTGCTGGGA
TTACAGGCATGAGCCACCACATCTGGCCCTACACTGGGATTTAAAGGGATCCCTTCTTGC
CTTCAACCCACATTGCCTTGAGATTAGAAGTGGCTTTGAGATTGAAGGTTAATATAAACA
TCTGAAGCTTAGATAAATGTACGTTTGTGTGGACTCCTTTGAGATCCTACCTTCAGGTGT
ATATGCTCACACATTTGTAATAGCACGTGCATCAGGCTGTTCCCTCCTACTCGAATGTCT
TATTTTCTATTTAACATAATCTAGTAGATGAAAAAGCATGGCTTGACCTGGGTAACAGCC
TTATGAGGAATATGGCCTTTTGGACTGTTGGACTGTTGAGGTTCTAGTAAGTGTGGACCT
GGCAGAAAGTGACCAGAACTTATGCTAATTTATTCATTTTATTTTATTTTTATTTTTTGA
GATAGGATCTCACTCTGTTGCCCAGGCTGGAGTGTAGTGGCACCATCTTGGCTCATTGCA
ACCTCCTCCTTCTAGGCTCAAGCGATCCTCCCACCTCAGCCTCCCCAGCAGCCAGGACTG
CAGGTGCACACCACCATGCCCAGCTAATTTTTATTTTATTTTTTGGTAGAGATGCGGTTT
CACCATGTTGGCCAGGCTGGTCTTGAACTCCTGGCCTCAAGTGATCTGCCTGCCTCGGCT
TCCCAAAGTGCTGGAATTACAGGCCTGAGCCACTGGACCTGGCCCAGAACTTATGCTAAT
TCAAAGTAAATTTTGGTATTTAAAGAGGCCAGCCTTGTAACTGCAAATCTGTGAAGTGAC
AATGTTGCAACATGGTAGTGAGGTAGGAGGCAGGGCTCAACTCCAGAAGCCAGAAGCGGG
GCTTGGGACAGCGGACCAAACTGAGGACTAACTAAAACAGGGATAGGATGGAAGCAGCTT
TTCATAAAACACATAAAACAGTGTGCCATATCAGTTTACCATTGCCATGGCAACACCTGG
AGTTAGCACCCCTTTCCATGGCAATGACCAGAGGACCCAAAAGTTACTACCCCTTCCCTA
GAAATGTCTGCATAAACCACCCGTTAGCCGGGCATGGTGGCTCACGCCTGTAATCCCAGC
ACTTTGGGAGGCTGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCC
AACATGGTGAAACCCATCTCTACCAAAAATACAAAAATTAGCTGGGCGTGGTGGTGGGCA
CCTGTAGTCTCAGCTACTCAGGAGACTGAGGCAGGAGAATCATTTGAATCCGGAGGCAGA
GGTTGCAGTGAGCCAAGATCGTGCTGCCATTGCACTCCAGCCTGGGTGACAAGAGCAAAA
CTCTGTCTGAATAAACAAACAAACAAACAAACAAAAACAAAAAAACCACCCCTTACTCTG
CATGTAACTAGAAGTGGGTATAAATATGACTACAAAACTGCCCTGAGCTGCTACTTTCTG
CCTATGGGGTAGCTCTTTTCTGCGGGAGCAGTCACAGAGCTGTGACACTGCTTCTTCAAT
AAAGCTGTTTTCTTCTCCCTCTGGCTTGCCCTTGAATTCTTTCCTGGGCAAAGCCAAGAA
CCTCTGCAGGCTAATCCCCGCTCTGGGGCTCACCTGCCCTACATGAGTAGTGCAAATTGT
AAATTTGCTAACAACAAATTGCCTCACATATTTTATTTTATTTATTTATTTTTTGAGATG
GATTCTTGCTCTGTCACCTAGGCTGGAGTGCAGTAGCGAGATTTCAGCTTGCTGCAACCT
CCACCTCCCGGGTTCAAGAGATTCTCCTGCCTAAGCCTCCCGAGTAGCTGGGATTACAGG
CACCCCCCACCACGCCTGACTAATTCTTGTATTTTTAGTAGAGATGGGGTTTTGCCATGT
TGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCTCCTCAGCCTCCCAAAG
TGTTAGGATTACAGGTGTGAACTACCACGCCTGGCCTGCCTCACAATTTTTTTTTTTTTT
TTTTTTTTTTTAGATGGAGTTTTGCTCTTGTTGCCCAGGCTGGAGTGCAATGGCGGGATC
TCGGCTCACCGCAACTTCCGTCTCCCCGGTTCAAACAATTCTCCTGCTTCAGCCTCCTGA
GTAGCTGGGATTGCAGGCATGCCCCACCACGCCCAGCTAATTTTGTATTTTTAGTAGAGA
CGGGGTTTCTCCATATTGGTCAGGCTGGTCTCCAACTCCCGACCTCAGGTGATCGCCCAC
CTCTGCCTCCCAAAGTGCTGGGATTAAGGCATGAGCCACTGCGCCCAGCCAGATTGATGG
ATTGATTGATTTTGAGATGGAGTTTCCCTCTTGTTGCCCAGGCTGGAGTGCAATGGTGCA
ATCTCAACTCACCTCAACCTCTGCCTCCCAGGTTCAAGCGACTCTCCTGCCTCAGCCTCT
GGAGTAGCTGGGATTACAGGCATGCGCCACCATGCCCGGCTAATTTTGTATTTTTAGTAG
AGACGGGGTTTCTCCATATTGGTCAGGCTGGTCGCGTTGGTCTGCCCGCCTCGGCCTCCC
GAAGTGCTGGGATTACAGGCATGAGCAACCGTGCCCGGCGCCTCACAGATTTTAAAAGCG
TAACTCTAAACTCATTGTTAGTCTAAAGTTATTGGGTTTTGATTTGCTTACATAATAGGG
TTTAAGGAAAGTCAGCAGTAAGTTTGGCTTGGTCATATTAATAATAGGAAATGAGCCTGA
GTAACATGGTGAAACTTCATCTCTACCAAAGAAAAATTCAAAAATTAGCCAGGTGTGGTG
GCACATGCCTGTAGCCCCAGCTACTTGGGAGGCTGAGGTGGGAAGATCTCTCGAGCCTGG
GAAGCAAAGGCTGCAGTGAGCCGAGATTGCACCACTGCAGTCCAGCCTGGGCAACAGAAT
GAGACCCTGTCTCAAAAAAATAATAATAATAGGAAGTGATTTTAAGGTTTTGGTCTCAAT
ACTTAAATATTTAAATATTGTTGAAAACCAGTAAAGCCTGGATCATATTGCATCTCAAAC
TAAAAACTGGAGTTCTAGATTTAAACACACACACACAAGCTTTTTTATTTGCAGCTGAGA
CTACAGGCATGTACCACTATGCCCAGCTGTTTTTTTGAGATATTTGTTTGTTTGTTCATT
TGTTTGTTTTTGAGATGGAGTTTTACTCCGTCCCCAGGCTACAGTGCAGTGGCTCGACCT
CAGCTCACTGCAACCTCCGCCTCCTGGGTTCAACTGATTCTCCTGCCTCAGCCCGACCCA
GGTGTGAGCCACCATGCCCAGCCTCAGCTGTTTTTATTTTTTTATAGAAATGGGGTCTTG
CTATGTTGTCCAGGCTGGTCTTGAACTCCTGGGCTCAAGTGATCCTCCCACCTTGGCCTC
CAGAAGTGTTGGGATTACAGGTATGAGCCACTGTGCCTGGCTACAAAAATTTTTTCTTAG
GATGAGGACATTTATACTATTGTTTTATTTTTGGTTGTTGTTGTTTGGGTTTTTTTTTTT
TTGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTCGCACGATCTCGGCTCAC
TGCAGCCTCCACCTCCTGGGTTCAAGCAATTCTCCTGCCACAGTCTCCCGAGTAGCTGGG
ATTACAGGGGTGCACCACCATGCCCAGCTAATTTTTGTTTTTCAGTAGAGATGGGGTTTT
GCCATGTTGCCCAGGCTGGTTTTGAACTCCTGACCTCAGGTGATCCACCTGCCTCTGCCT
CCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGGCTGGCAGAATCACGTCTCATCTC
TAACTCCTCTCCTTCCTCCTCCCTCTCCCCGATTCTGCGGCAGATACACTAGGCTCCTCA
GAGTTCCCGAAACACACTGGCACACCCTTCCTCAGAGTCCCAGGGCTCCCTGGATTTCTG
CCTTAAACTATTTTCCCAGAAATCTGTGTGGCTTGATTCTTTACTTCTTTCAGCTCCCCG
CTGAGACGTCACCTGGCCATTATTTAAAATAGTGGTGTTTATTTCTAGCTACATAATATG
CTCAAAGGCAGTAAGTGGAACTGGGATTCCAAACCCTGATCTTCATCTTCTTAGCATTCC
ATGTTTCCCTGTGGAACTCTTCTTTAAAGCTTATTTAAGAATTCTAGCCGAGCAGGGTGG
CTCATGTCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGAGAGGATTGCTTGAGCCCAAG
AGTTCGAGACCAACCTGGGCAACATAGTGAGACTTGATCTCTACAAAAAAATATTTAAAA
CATTTCCAGGCATGGTGGCATGTGCCTGTAGTCCCAGCTATTCGAGAGGCTGAGATAGGA
GAATCACTTGAGCCTGAAAGGTTGAGGCTACAGTGAGCCATGATTGCACCACTGCACTTC
AGCCTGGGTGACAGAATGAGATCCTGTCTCAAAAAAAGAAAAAAATTATAAATACATAGT
AGTATATAGCTGGGTGTGGTgatgcaagcctgtaattccagttaCTCAGGAGACTGAGGC
AAGAGAATTGCTTGAACCCGGGAGTGGAGGTTGCAGTGAGCTGAAATCGTGCCACTGCTC
TCCCCAACCTGGGCGACAGAGTGAGACTGTGTCTCGGAAAAAAAAAAAGAAAAAAAAAAG
TATATACGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATATAGAGAGAGAGAGAGA
GAGAGGTATATACATGAATCCAGTGGTTTTTGAGTTTTGTTTTCATTCTTGTTGAGAAAC
TGTTCAAATGCTCTCTTAATTCAAAGTGTAAATACATAAGGCAGAAAAAGGCAGAGTTAT
GACTGAGGCTGGGTTGGGGGGCCTAAGCCCTGTCCCTTTGGTTTTCTTTTTCTTTCTTTT
TTTTTGAGATGGAGTCTCGCTCTGTTGCTCAGGCTGGAGTGCAGTGGTGTGATCTTGGCT
CACTGCAACCTCCGCCTCCTGGGTTCAAGCAATTCTCCTACTTCAGCCTCCAAAGTAGCT
GGGATTACAGGTATGTGCCACCATGCCCGGCTAATTTTGTATTTTTAGTAGAGATGGGGT
TTCTACATGTTGATCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCGCCCTCCTCAG
CCTCCCAAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCTGGCCTACAGTTTTTATT
TTTTTATAGAGACAGGGTCTTGCTATGTTGCCCAGGCTGGTCTCAAACTCCTAAGCTCAA
ACAATCCTCCTGTCTTCTGTGTCCCAAAGTGCTGGAATTACTGCACCTGGCATTTGCAAA
CTTTTTAATCAGGCTGTGGTTGGCAGTTTGCCAAGACGATTCCTTGTAGATCTGATTTTG
GCAGCAAACAACATAGAAGTCGTACAGGAAATGCTAACAATTACATGTGGTGATTTTGAG
AACAGCTACCAAATTCTTCACTTTTGTATCTCAAGCGAATGTTCAAATATTTTTAAAAAT
TATTTTTAAGGTATTGACTTTGCCACTCGTAAAATAGCCAAGTTGCTGAAGCCACAGAAA
GTGATTGAGCAGAATGGGGATTCTTTTACCATCCACACGAACAGCAGCCTAAGGAACTAC
TTTGTGAAATTTAAAGTTGGAGAAGAATTTGATGAAGATAACAGAGGCCTGGACAACAGA
AAATGCAAGGTAAAAgatgcaagcctgtaattccagttaGATTACGCTTGTAATCCTAAC
ACTTTGGGAGGCCAACGCAGGCGGACCACCTGAGGTCAGTAGTTTGAGACCAGCCTGGGC
AACACGGCAAAACCCTGTCTCTACAGAAAAAAATTCAAAAAGTAGGGGGGCGTGCTGGCA
GGAGCCTGTAATCCCAGCTACTTAGGAGGCTGAGGCAGGAGAATCACTTGAACCCGGGAG
GTGGAGGTTGGTTGCAGTAAGCCAAGATCGTGCCACTGCACTCCAGCCTGGGTGACAGAG
TGGGACTCCATCTCAAAAAAAAAAAAAAGCAGTAAGTAGGCTGTTGATTTTGCAAGGGTA
ACTTGGCATTCTACTTCGTAACACTTGAGGATCCTGCCAGGACAAGCTAACATTTTCTCC
TCTCTTCATGCAGAGTTTGGTTATCTGGGACAATGACAGGCTCACCTGTATCCAGAAGGG
AGAAAAGAAGAACAGAGGCTGGACCCATTGGATCGAAGGAGACAAACTCCACCTGGTATC
CACCACATTTTGTTCTTAATGAGATGATACAGTATTAAAGGAAACATCAGGCCAAGCGTG
GTGGCTCACACCTGTAATCCCAGCATTTTAGGAGGCCGAGGTGGGTGTATCACTTGAGGT
CAGGAGACTAGCCTGGCCAACATGGTGAAACCCCATCTCTACTATTTTTTTTTTTTTTTT
GAGATGGAGTATCGCTGTGTCACCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGC
AACCTCCACCTCCTGGGTCCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACT
ACAGGCACGCACCACCACACCCAGCTAATTTTTGTATTTTTAGTGGAGACGGGGTTTCAC
CATGTTGGCCAGGATGGTCTCGATCTCTTGACCTCATGATCCACCCGCCTCGGCCTCCCA
AAGTGCTGGGATTACAGGCATGAGCCACCACCACACCTGGCCCATCTCTACTGAAAATAC
AAAAATTAGCCGGGCATAGTGGCGCATGCCTATACTCACTCTCATCTTATATTAAATGAA
ACAGCCGAATATTCCGACAGAGGCAGGAAGATAACAgatgcaagGctgtaaGtccagtta
TACCTATTATATGTAATAGCTACTTTATGTATACATAGATATGCATAGATAGATATAGTA
GCTCACATCTTTGGAGTGATTATTTTGGGCCCAATTACTGTGCTCAATCCTTTGAGTGCA
TTATCTCATCTAATCTTCACAACCCTGTGAAAAGGACGCCATTTTTCCCATTCACAAATA
AATTGGGATTTTGAAATTCCCCAAGGCTGCTGTCAGAAGCATCAGAATCCAGTTTAAAAG
GGTTTATTCAGACTGGGCGAGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGA
CGTGGGCGGATCACGAGGTCAGGAGATCAAGATCATCCTGGCCAACATGGTGAAACCCCG
TCTCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGCACATGTCTGTAATCCCAGCTA
CTTGGGAGGCTGAGGCAGGAGAATTGCTAGAACCAGTTAGTCGGAGGTTGCAGTGAGCCA
AGATCGCACCACTGCCCTACGGCCTGGTGACAGAGGCCGTTTCAAAAAAAAATAAAACAA
AATAAGGGTTTATTCAGGCATGAAGATGAGAATGGCCACCCAGGAAACACAGACTCCAAA
GAAATGGGGTCAGTACACCCAAGCTGAAAAGTTAATGTCTTATTTTTTTTTTTTTTTTGA
GATGGAGTCTCTCCCTCTGTCACCCAGTGTCACCCACGCTGGAGTGCAGTGGTGTGATCT
CAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCGATCCTCCCACCTCAGCCTCCCGAG
TAGCTGGGACTACAGGCATGCACCACCACACCCAGCTAGTTTTTGTATTTTTAGCAGAAA
CGGGATTTTACCATATTGGCCAGGCTGGTCTCGAACaatgcaagcctgtaattccagttg
CCTGGGCCTCCCAAAGTGTTGGGATTACAGGCGTGGCCGCTTGTAATAAAAATTTAATTT
CTTGGAATGTAATTCTTGGAGTTTTTCTTTTCCTTTCTTTTTCTTTTTCTTCTTTTACTT
TTAAGCTGTTGGACTTGAGGTGTTTTTCTTTAATGGCTTTATTGAGGTATACTTTATGTA
CCAAAAAATGCACCTGTTTTAAGTGTACAGTTTGATAATTT