| checking alternative consensus for artificial reads | 0.17 sec | Passed |
| checking extraction of reference from reads | 0.55 sec | Passed |
| checking mapping to targets for artificial reads | 0.71 sec | Passed |
| checking realigned reads for artificial input | 0.96 sec | Passed |
| checking realigned reads for artificial input using knowns | 1.2 sec | Passed |
| checking realigned reads for artificial input using knowns and reads | 1.2 sec | Passed |
| checking realigned reads for artificial input with reference file | 1.4 sec | Passed |
| extract seq/qual from a read with clipped bases at end | 1 ms | Passed |
| extract seq/qual from a read with clipped bases at start | 1 ms | Passed |
| extract seq/qual from a read with no clipped bases | 1 ms | Passed |
| get cigar and coordinates for read that falls wholly after deletion | 0 ms | Passed |
| get cigar and coordinates for read that falls wholly after insertion | 0 ms | Passed |
| get cigar and coordinates for read that falls wholly before insertion | 0 ms | Passed |
| get cigar and coordinates for read that partially spans insertion, clipped bases at end | 0 ms | Passed |
| get cigar and coordinates for read that partially spans insertion, clipped bases both ends | 1 ms | Passed |
| get cigar and coordinates for read that partially spans insertion, no clipped bases | 0 ms | Passed |
| get cigar and coordinates for read that spans deletion, clipped bases at start | 0 ms | Passed |
| get cigar and coordinates for read that spans indel, no clipped bases | 0 ms | Passed |
| if realigning a target doesn't improve the LOD, don't drop reads | 0.56 sec | Passed |
| if unclip is selected, don't drop base when extracting from a read with clipped bases | 1 ms | Passed |
| map reads to targets | 10 ms | Passed |
| realign a read with an insertion that goes off the end of the read | 1 sec | Passed |
| realign reads to an insertion | 0.91 sec | Passed |
| skip realigning reads if target is highly covered | 0.93 sec | Passed |
| skip realignment if target is an insufficient LOD improvement | 0.98 sec | Passed |
| test OP and OC tags | 1.2 sec | Passed |
| test mismatch quality scoring | 0 ms | Passed |
| test mismatch quality scoring after unpacking read | 0.17 sec | Passed |
| test mismatch quality scoring for no mismatches | 0 ms | Passed |
| test mismatch quality scoring for offset | 0 ms | Passed |
| test mismatch quality scoring with early exit | 0 ms | Passed |
| we shouldn't try to realign a region with no target | 2 ms | Passed |
| we shouldn't try to realign reads with no indel evidence | 0.58 sec | Passed |
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