| CIGAR with N operator | 2 ms | Passed |
| CIGAR with P operators | 2 ms | Passed |
| CIGAR with multiple N operators | 2 ms | Passed |
| CIGAR/MD tag mismatch should cause errors | 1 ms | Passed |
| Get correct matches base from MDTag and CIGAR with N | 1 ms | Passed |
| Get correct matches for MDTag with mismatches and deletions | 6 ms | Passed |
| Get correct matches for mdtag with insertion | 1 ms | Passed |
| Get correct matches for mdtag with insertion between mismatches | 0 ms | Passed |
| Get correct matches for mdtag with intron and deletion between mismatches | 1 ms | Passed |
| Get correct matches for mdtag with intron between mismatches | 1 ms | Passed |
| Get correct matches for mdtag with mismatch, insertion and deletion | 3 ms | Passed |
| Get correct matches for mdtag with mismatches and insertion | 2 ms | Passed |
| Get correct matches for mdtag with mismatches, insertion and deletion | 3 ms | Passed |
| Throw exception when number of deleted bases in mdtag disagrees with CIGAR | 1 ms | Passed |
| check complex mdtag | 4 ms | Passed |
| check that mdtag and rich record return same end | 0 ms | Passed |
| create new md tag from read vs. reference, alignment with deletion | 0 ms | Passed |
| create new md tag from read vs. reference, alignment with insert | 0 ms | Passed |
| create new md tag from read vs. reference, perfect alignment match, 1 mismatch | 0 ms | Passed |
| create new md tag from read vs. reference, perfect match | 0 ms | Passed |
| get correct string out of complex mdtag | 0 ms | Passed |
| get correct string out of mdtag with deletion at end | 1 ms | Passed |
| get correct string out of mdtag with mismatches at end | 0 ms | Passed |
| get correct string out of mdtag with mismatches at start | 0 ms | Passed |
| get correct string out of mdtag with no mismatches | 0 ms | Passed |
| get end of read with mismatches and a deletion at end | 0 ms | Passed |
| get end of read with no mismatches or deletions | 1 ms | Passed |
| get end of read with no mismatches, but a deletion at end | 0 ms | Passed |
| get gapped reference | 1 ms | Passed |
| get start of read with mismatches at the start | 0 ms | Passed |
| get start of read with no mismatches or deletions | 0 ms | Passed |
| get start of read with no mismatches, but with a deletion at the start | 0 ms | Passed |
| handle '=' and 'X' operators | 1 ms | Passed |
| md tag equality and hashcode | 2 ms | Passed |
| md tag invalid base | 0 ms | Passed |
| md tag pure insertion equality | 0 ms | Passed |
| md tag with non-digit initial value | 0 ms | Passed |
| md tag, pure insertion | 0 ms | Passed |
| md tag, pure insertion, test 2 | 1 ms | Passed |
| move a cigar alignment by two for a read | 11 ms | Passed |
| null md tag | 0 ms | Passed |
| rewrite alignment to all matches | 0 ms | Passed |
| rewrite alignment to include a deletion but otherwise all matches | 1 ms | Passed |
| rewrite alignment to include an insertion at the start of the read but otherwise all matches | 0 ms | Passed |
| rewrite alignment to two mismatches followed by all matches | 0 ms | Passed |
| valid md tags | 9 ms | Passed |
| zero length md tag | 0 ms | Passed |
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