net.maizegenetics.dna.tag

Class SAMUtils

net.maizegenetics.dna.tag.SAMUtils

public class SAMUtils

Method Detail

getVariants

public static java.lang.String[] getVariants(java.lang.String inputLine)

Parses an input line from a SAM file to determine all variants.

Parameters:

inputLine - A line from a SAM file.

Returns:

org.jetbrains.dokka.NodeRenderContent@5dc329bc: A 3 X (number of variants) array holding all SNPs, insertions and deletions from both the CIGAR field and the MD:Z: field.

adjustCoordinates

public static kotlin.Array[] adjustCoordinates(java.lang.String cigarString,
                                               int startCoordinate)

Uses a CIGAR code and the start coordinate of a BWA alignment to find the corresponding end coordinate. Adjusts start coordinate if beginning of alignment was soft clipped.

Parameters:

cigarString -

startCoordinate -

endCoordinate

public static long endCoordinate(java.lang.String cigarString,
                                 long startCoordinate)

Uses a CIGAR code and the start coordinate of a BWA alignment to find the corresponding end coordinate.

Parameters:

cigarString -

startCoordinate -

parseCIGAR

public static java.lang.String[] parseCIGAR(java.lang.String cigarString,
                                            java.lang.String tagSequence)

Searches a CIGAR string for insertions in the reference sequence.

Parameters:

cigarString - The text of the CIGAR string.

tagSequence - The sequence of the CIGAR string's corresponding tag.

Returns:

org.jetbrains.dokka.NodeRenderContent@dbce4b9: variant A 3x(number of variants) array containging:
[0]The character "+" [1]The character "-" [2]The position of the reference insertion relative to the tag.

parseMDField

public static java.lang.String[] parseMDField(java.lang.String mdField,
                                              java.lang.String tagSequence)

Decodes the MD: field in a SAM file to determine the location of polymorphisms and whether they are mismatches or deletions from the reference sequence.

Parameters:

mdField - The text of the MD: field, NOT including the MD:Z: prefix!

tagSequence - The sequence of the tag corresponding to mdField.

Returns:

org.jetbrains.dokka.NodeRenderContent@71f93b2b: variant A 3x(number of variants) array containing:
[0] Reference haplotype
[1] Tag haplotype
[2] Position in tag
If there are no polymorphisms in the alignment, the method returns NULL.