public Tags
Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.
Tags are encoded in longs with a 2-bit encoding see the package description for details class BaseEncoder
class BaseEncoderint getTagSizeInLong()
Returns the number of longs use to represent the sequence
java.lang.String getNullTag()
Returns a polyA string of length 32*getTagSizeInLong()
int getTagLength(int index)
Returns the length in bp of a particular tag
index - kotlin.Array[] getTag(int index)
Get the compressed read sequence in a long array for a given index
index - int getTagIndex(kotlin.Array[] read)
Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.
read - as a compressed long arraykotlin.Array[] getTagIndexSet(kotlin.Array[] read)
Gets the set indices of matching reads (the only one if a unique list). If the read is not found then it returns a null array indicating its insertion point.
read - as a compressed long arrayboolean areTagsUnique()
Reports whether this list of reads includes duplicates True is there are no read duplicates, false otherwise. Collapses read files are likely to be unique While a virtual digest of a genome with contain some duplicates
int getTagCount()
This is the number of different tags in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct tags if readUnique is true