countVariants(VCFview, FeatureVector) |  | 0% |  | 0% | 19 | 19 | 48 | 48 | 1 | 1 |
makeFeature(VCFRecord, String, VCFview, FeatureVector, Bases, Entry, Key, AbstractVCFReader, int) |  | 0% |  | 0% | 9 | 9 | 28 | 28 | 1 | 1 |
exportFasta(VCFview, FeatureVector, boolean, Writer) |   | 59% |   | 50% | 29 | 34 | 26 | 77 | 0 | 1 |
createFeatures(VCFview, EntryGroup) |  | 0% |  | 0% | 6 | 6 | 26 | 26 | 1 | 1 |
count(VCFRecord, int[], FeatureVector, AbstractVCFReader, int, VCFview) |  | 0% |  | 0% | 8 | 8 | 17 | 17 | 1 | 1 |
exportFastaByRange(VCFview, Selection, boolean, Writer) |   | 57% |   | 45% | 9 | 11 | 19 | 52 | 0 | 1 |
getBasesInRegion(AbstractVCFReader, int, String, int, int, String, FeatureVector, VCFview, boolean, boolean, boolean) |   | 44% |   | 35% | 8 | 11 | 10 | 26 | 0 | 1 |
getFile(String, int, String, JComponent) |  | 0% |  | 0% | 6 | 6 | 16 | 16 | 1 | 1 |
getAllBasesInRegion(AbstractVCFReader, int, int, int, String, FeatureVector, VCFview, boolean, boolean, boolean) |   | 20% |   | 6% | 8 | 9 | 13 | 16 | 0 | 1 |
storeVCFRecords(VCFview, HashMap[], int, int) |   | 38% |   | 25% | 8 | 11 | 12 | 19 | 0 | 1 |
export(Map, List, VCFview) |  | 0% |  | 0% | 3 | 3 | 10 | 10 | 1 | 1 |
writeVariants(VCFview, HashMap[], Writer[], FeatureVector, int, int, int, Bases, int) |   | 83% |   | 70% | 15 | 31 | 10 | 75 | 0 | 1 |
exportVariantFasta(VCFview) |  | 0% |  | 0% | 2 | 2 | 17 | 17 | 1 | 1 |
writeOrView(AbstractVCFReader, Feature, Writer, StringBuffer, String) |   | 39% |   | 50% | 3 | 5 | 8 | 17 | 0 | 1 |
makeFeatures(AbstractVCFReader, int, String, int, int, FeatureVector, VCFview, Bases, Entry) |  | 0% |  | 0% | 2 | 2 | 8 | 8 | 1 | 1 |
getBaseDirectoryFromEntry(Entry) |  | 0% |  | 0% | 6 | 6 | 12 | 12 | 1 | 1 |
maskSites(int, int, int, boolean, String) |  | 0% |  | 0% | 3 | 3 | 7 | 7 | 1 | 1 |
writeVCF(Map, String, int, VCFview, FeatureVector, int) |  | 0% |  | 0% | 2 | 2 | 9 | 9 | 1 | 1 |
getSeqsVariation(VCFRecord, String, int, boolean, boolean) |   | 89% |   | 78% | 10 | 24 | 5 | 50 | 0 | 1 |
getFeatures(FeaturePredicate, EntryGroup) |  | 0% |  | 0% | 3 | 3 | 8 | 8 | 1 | 1 |
isSNPorNonVariant(VCFRecord) |  | 0% |  | 0% | 4 | 4 | 1 | 1 | 1 | 1 |
writeOrView(Writer, StringBuffer, String, StringBuffer, int) |   | 32% |   | 25% | 2 | 3 | 4 | 6 | 0 | 1 |
exportVariantFasta(VCFview, PrintWriter, int, FeatureVector, Bases) |   | 94% |   | 94% | 1 | 10 | 4 | 41 | 0 | 1 |
isBCF(String) |   | 82% |   | 66% | 2 | 4 | 3 | 14 | 0 | 1 |
loadRecords(HashMap, AbstractVCFReader, String, int, int, int) |   | 84% |   | 75% | 1 | 3 | 1 | 5 | 0 | 1 |
IOUtils() | | 0% | | n/a | 1 | 1 | 1 | 1 | 1 | 1 |
writeOrViewRange(AbstractVCFReader, int, int, int, Writer, StringBuffer, MarkerRange, Bases, String, VCFview, EntryGroup, boolean, boolean) |  | 100% |   | 90% | 1 | 6 | 0 | 25 | 0 | 1 |
writeSequence(Writer, StringBuffer, String, int) |  | 100% |   | 75% | 2 | 5 | 0 | 12 | 0 | 1 |
getHeader(AbstractVCFReader, MarkerRange, String, int, int) |  | 100% |   | 83% | 1 | 4 | 0 | 8 | 0 | 1 |
wrapString(String, StringBuffer) |  | 100% |  | 100% | 0 | 3 | 0 | 7 | 0 | 1 |
getBase(String, boolean) |  | 100% |  | 100% | 0 | 2 | 0 | 3 | 0 | 1 |
static {...} |  | 100% | | n/a | 0 | 1 | 0 | 2 | 0 | 1 |