| countOverRange(BamView, String, int, int, int, int[][]) |  | 0% |  | 0% | 12 | 12 | 29 | 29 | 1 | 1 |
| calc(BamView, String, int, boolean, JProgressBar) |   | 39% |   | 20% | 13 | 16 | 18 | 30 | 0 | 1 |
| getCount(BamView, int, int, String, boolean, boolean) |   | 37% |   | 4% | 12 | 13 | 17 | 29 | 0 | 1 |
| getIndexFile(String) |   | 74% |   | 66% | 8 | 13 | 6 | 45 | 0 | 1 |
| validateSAMFile(SamReader, CRAMReferenceSequenceFile, boolean) |  | 0% |  | 0% | 2 | 2 | 10 | 10 | 1 | 1 |
| createIndexFileFromScratch(String, File) |   | 81% |   | 60% | 4 | 6 | 4 | 25 | 0 | 1 |
| getFtpBufferSize() |  | 0% |  | 0% | 2 | 2 | 5 | 5 | 1 | 1 |
| calculateMappedReads(BamView, FeatureVector, boolean, boolean, boolean, int[], JProgressBar) |   | 92% |   | 81% | 3 | 9 | 3 | 32 | 0 | 1 |
| getFtpSocketTimeout() |   | 34% |   | 50% | 1 | 2 | 2 | 5 | 0 | 1 |
| count(BamView, String, int, int, boolean, boolean, boolean) |   | 95% |   | 64% | 4 | 8 | 1 | 21 | 0 | 1 |
| samRecordEqualityCheck(SAMRecord, SAMRecord) |   | 88% |   | 66% | 3 | 7 | 1 | 9 | 0 | 1 |
| isCramFile(String) |   | 75% | | n/a | 0 | 1 | 2 | 6 | 0 | 1 |
| isBamFile(String) |   | 75% | | n/a | 0 | 1 | 2 | 6 | 0 | 1 |
| BamUtils() |  | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
| getFeatureLength(Feature) |  | 100% |  | 100% | 0 | 2 | 0 | 6 | 0 | 1 |
| constructIndexFilename(String) |  | 100% |  | 100% | 0 | 3 | 0 | 6 | 0 | 1 |
| createTempIndexFile(URL) |  | 100% |  | 100% | 0 | 3 | 0 | 9 | 0 | 1 |
| static {...} |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |