net.maizegenetics.analysis.gobii

Class GOBII_IFLUtils

net.maizegenetics.analysis.gobii.GOBII_IFLUtils

public class GOBII_IFLUtils

This class contains utility methods for pulling values out of hmp or vcf files needed when creating the intermediate files for loading into GOBII postgres and monetdb instances

Method Detail

getChromFromLine

public static int getChromFromLine(java.lang.String mline,
                                   boolean isVCF,
                                   kotlin.Array[] tabPos)

getMarkerNameFromLine

public static java.lang.String getMarkerNameFromLine(java.lang.String mline,
                                                     boolean isVCF,
                                                     kotlin.Array[] tabPos,
                                                     java.lang.String mapsetname)

getPosFromLine

public static int getPosFromLine(java.lang.String mline,
                                 boolean isVCF,
                                 kotlin.Array[] tabPos)

getStrandFromLine

public static java.lang.String getStrandFromLine(java.lang.String mline,
                                                 boolean isVCF,
                                                 kotlin.Array[] tabPos)

addMonetdbVariantData

public static java.lang.String addMonetdbVariantData(java.lang.String ref,
                                                     java.lang.String altsOrig,
                                                     java.lang.String mline,
                                                     boolean isVCF,
                                                     kotlin.Array[] tabPos)

getAltsForRef

public static java.lang.String getAltsForRef(java.lang.String ref)

getAltsFromLine

public static java.lang.String getAltsFromLine(java.lang.String mline,
                                               java.lang.String ref,
                                               boolean isVCF,
                                               kotlin.Array[] tabPos)

splitIFLFile

public static void splitIFLFile(java.lang.String infile,
                                java.lang.String outdir,
                                int maxSize)

This method is created to break up very large files that GOBII can't handle. For example: one dataset has 83M+ lines. Takes GOBII overnight just to load the marker_linkage_group or dataset_marker data. Yaw suggests we break it into files of size 10M. So pass in the file, give an output directory, and split the file into smaller files. Each smaller file must retain the header, and it must end with the same table name (e.g. DS_4.marker_linkage_gropu must still

Parameters:

infile -

outdir -

maxSize -