Package | Description |
---|---|
htsjdk.samtools.util | |
htsjdk.variant.vcf |
Modifier and Type | Method and Description |
---|---|
static IntervalList |
IntervalList.concatenate(Collection<IntervalList> lists)
A utility function for merging a list of IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.copyOf(IntervalList list)
creates a independent copy of the given IntervalList
|
static IntervalList |
IntervalList.difference(Collection<IntervalList> lists1,
Collection<IntervalList> lists2)
A utility function for finding the difference between two IntervalLists.
|
static IntervalList |
IntervalList.fromFile(File file)
Parses an interval list from a file.
|
static IntervalList |
IntervalList.fromFiles(Collection<File> intervalListFiles)
Calls
fromFile(java.io.File) on the provided files, and returns their union(java.util.Collection) . |
static IntervalList |
IntervalList.fromName(SAMFileHeader header,
String sequenceName)
Creates an IntervalList from the given sequence name
|
static IntervalList |
IntervalList.fromReader(BufferedReader in)
Parses an interval list from a reader in a stream based fashion.
|
static IntervalList |
IntervalList.intersection(Collection<IntervalList> lists)
A utility function for intersecting a list of IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.intersection(IntervalList list1,
IntervalList list2)
A utility function for generating the intersection of two IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.invert(IntervalList list)
inverts an IntervalList and returns one that has exactly all the bases in the dictionary that the original one does not.
|
IntervalList |
IntervalList.padded(int padding)
Returns a new IntervalList where each interval is padded by 'padding' bases on each side.
|
IntervalList |
IntervalList.padded(int before,
int after)
Returns a new IntervalList where each interval is padded by the specified amount of bases.
|
IntervalList |
IntervalList.sorted()
returns an independent sorted IntervalList
|
static IntervalList |
IntervalList.subtract(Collection<IntervalList> lhs,
Collection<IntervalList> rhs)
A utility function for subtracting a collection of IntervalLists from another.
|
static IntervalList |
IntervalList.subtract(IntervalList lhs,
IntervalList rhs)
A utility function for subtracting a single IntervalList from another.
|
static IntervalList |
IntervalList.union(Collection<IntervalList> lists)
A utility function for finding the union of a list of IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.union(IntervalList list1,
IntervalList list2) |
IntervalList |
IntervalList.uniqued()
Returned an independent IntervalList that is sorted and uniquified.
|
IntervalList |
IntervalList.uniqued(boolean concatenateNames)
Returned an independent IntervalList that is sorted and uniquified.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
IntervalUtil.contains(IntervalList intervalList,
String sequenceName,
long position)
Return true if the sequence/position lie in the provided interval list.
|
static IntervalList |
IntervalList.copyOf(IntervalList list)
creates a independent copy of the given IntervalList
|
static List<Interval> |
IntervalList.getUniqueIntervals(IntervalList list,
boolean concatenateNames)
Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
|
static List<Interval> |
IntervalList.getUniqueIntervals(IntervalList list,
boolean concatenateNames,
boolean enforceSameStrands)
Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
|
static IntervalList |
IntervalList.intersection(IntervalList list1,
IntervalList list2)
A utility function for generating the intersection of two IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.invert(IntervalList list)
inverts an IntervalList and returns one that has exactly all the bases in the dictionary that the original one does not.
|
static IntervalList |
IntervalList.subtract(IntervalList lhs,
IntervalList rhs)
A utility function for subtracting a single IntervalList from another.
|
static IntervalList |
IntervalList.union(IntervalList list1,
IntervalList list2) |
Modifier and Type | Method and Description |
---|---|
static IntervalList |
IntervalList.concatenate(Collection<IntervalList> lists)
A utility function for merging a list of IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.difference(Collection<IntervalList> lists1,
Collection<IntervalList> lists2)
A utility function for finding the difference between two IntervalLists.
|
static IntervalList |
IntervalList.difference(Collection<IntervalList> lists1,
Collection<IntervalList> lists2)
A utility function for finding the difference between two IntervalLists.
|
static IntervalList |
IntervalList.intersection(Collection<IntervalList> lists)
A utility function for intersecting a list of IntervalLists, checks for equal dictionaries.
|
static IntervalList |
IntervalList.subtract(Collection<IntervalList> lhs,
Collection<IntervalList> rhs)
A utility function for subtracting a collection of IntervalLists from another.
|
static IntervalList |
IntervalList.subtract(Collection<IntervalList> lhs,
Collection<IntervalList> rhs)
A utility function for subtracting a collection of IntervalLists from another.
|
static IntervalList |
IntervalList.union(Collection<IntervalList> lists)
A utility function for finding the union of a list of IntervalLists, checks for equal dictionaries.
|
Constructor and Description |
---|
IntervalListReferenceSequenceMask(IntervalList intervalList) |
SamLocusIterator(SamReader samReader,
IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments.
|
SamLocusIterator(SamReader samReader,
IntervalList intervalList,
boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments
|
Modifier and Type | Method and Description |
---|---|
static IntervalList |
VCFFileReader.fromVcf(File file)
Parse a VCF file and convert to an IntervalList The name field of the IntervalList is taken from the ID field of the variant, if it exists.
|
static IntervalList |
VCFFileReader.fromVcf(File file,
boolean includeFiltered) |
static IntervalList |
VCFFileReader.fromVcf(VCFFileReader vcf)
Converts a vcf to an IntervalList.
|
static IntervalList |
VCFFileReader.fromVcf(VCFFileReader vcf,
boolean includeFiltered) |