public class PETagsOnPhysicalMapV3 implements Tags
This class hold the multiple mapping positions of PE tags, including forward and backward PE tags. Data in this class are used to annotate HDF5TOPM When contig exist, the forward and backword tags are the contig and reverse complement of the contig, respectively. The PE tags were first aligned with bowtie2 (-k N), any number of mapping position can be imported PE tags of both end are stored in one long array with variable length, then they were truncated to 2 longs. This is easy for searching Using a pairIndex, each 64 bp tag has a index pointing to the other end of PE. It is worth noting that, the 64 bp tags are not unique. Rarely, there are multiple identical 64 bp tags, although the full length PE tags are unique. When multiple identical 64 bp tags exist, the one with longest full length PE is used to annotate HDF5TOPM.
public PETagsOnPhysicalMapV3(java.lang.String PETOPMFileS)
Constructor from a file
PETOPMFileS - public PETagsOnPhysicalMapV3(java.lang.String fFastaFileS,
java.lang.String bFastaFileS,
java.lang.String fSamFileS,
java.lang.String bSamFileS)
Constructor using fasta files and sam files
fFastaFileS - bFastaFileS - fSamFileS - bSamFileS - public void trancateTag()
Full length PE tags are truncated to certain size (2 longs in GBS Build V3.0)
public void writeBinaryFile(java.lang.String outfileS)
Write to a file
outfileS - public void readBinaryFile(java.lang.String infileS)
read from a file
infileS - public int getTagSizeInLong()
public int getVariableTagSizeInLong(int index)
public java.lang.String getNullTag()
public int getTagLength(int index)
public kotlin.Array[] getTag(int index)
public int getPairIndex(int index)
Return the index of the tag which is the other end of PE
index - public int getMappingNum(int index)
Return the number of mapping (multiple alignments)
index - public byte getChr(int tagIndex,
int mappingIndex)
Return chromosome of a mapping
tagIndex - mappingIndex - public byte getStrand(int tagIndex,
int mappingIndex)
Return strand of a mapping
tagIndex - mappingIndex - public int getStartPos(int tagIndex,
int mappingIndex)
Return start position of a mapping
tagIndex - mappingIndex - public short getScore(int tagIndex,
int mappingIndex)
Return score of a mapping
tagIndex - mappingIndex - public byte getDivergence(int tagIndex,
int mappingIndex)
Return divergence of a mapping
tagIndex - mappingIndex - public int getTagIndex(kotlin.Array[] read)
This may return one of multiple identical 64 bp tags, which are essentially differnt in full-length PE tags
read - public int getTagIndexWithLongestSeq(kotlin.Array[] read)
Return the index of 64 bp tag with alignment of longest PE tag, when there are multiple identical 64 bp tags. When the tag is not found, return -1
read - public kotlin.Array[] getTagIndexSet(kotlin.Array[] read)
Return the range of identical 64 bp tags, [0,3] means {0,1,2} are identical. When the read doesn't exist, return null
read - public boolean areTagsUnique()
public int getTagCount()
public void swap(int index1,
int index2)
public int compare(int index1,
int index2)
public void sort()
Sort the class based on 64 bp tags