| checking alternative consensus for artificial reads | 0.18 sec | Passed |
| checking extraction of reference from reads | 0.54 sec | Passed |
| checking mapping to targets for artificial reads | 0.57 sec | Passed |
| checking realigned reads for artificial input | 1 sec | Passed |
| checking realigned reads for artificial input using knowns | 1.4 sec | Passed |
| checking realigned reads for artificial input using knowns and reads | 1.1 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 | 0 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 | 0.54 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 | 4 ms | Passed |
| realign a read with an insertion that goes off the end of the read | 0.96 sec | Passed |
| realign reads to an insertion | 1.8 sec | Passed |
| skip realigning reads if target is highly covered | 1.8 sec | Passed |
| skip realignment if target is an insufficient LOD improvement | 2.4 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 | 0.16 sec | Passed |
| test mismatch quality scoring for no mismatches | 0 ms | Passed |
| test mismatch quality scoring for offset | 1 ms | Passed |
| test mismatch quality scoring with early exit | 0 ms | Passed |
| we shouldn't try to realign a region with no target | 1 ms | Passed |
| we shouldn't try to realign reads with no indel evidence | 0.61 sec | Passed |
![[Jenkins]](/jenkins/static/7165055c/images/jenkins-header-logo-v2.svg){kind=logo}
