net.maizegenetics.pangenome.hapCalling

Class ConvertGBSUtils

java.lang.Object

net.maizegenetics.pangenome.hapCalling.ConvertGBSUtils

public class ConvertGBSUtils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	configFile
static String	configFileName
static String	genomeVersionName
static String	hapidCountFilename
static String	hapidCountMapFileName
static String	methodIdName
static int	minTaxaPerRange
static String	readFileName
static String	samFileName

Constructor Summary

Constructors

Constructor and Description
ConvertGBSUtils()

Method Summary

Modifier and Type	Method and Description
static void	basicConverterTest()
static HaplotypeGraph	buildHaplotypeGraph()
List<HaplotypeNode>	chooseBestNode(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
static boolean	contains(String name, net.maizegenetics.taxa.TaxaList taxa)
static boolean	containsW22(net.maizegenetics.taxa.TaxaList taxa)
static void	countNodesWithW22(List<HaplotypeNode> myNodes)
static void	countSeqCharInPHG()
static void	countW22NodesFullGraph(HaplotypeGraph hapgraph)
void	evaluateOneBestNodeRanges(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
static void	howManyAnchorsHaveW22InMostFrequentNode(HaplotypeGraph hapgraph, com.google.common.collect.Multiset<Integer> hapidCounts)
static void	listBadNodes(String comp, String outfile)
static void	listTaxa(HaplotypeGraph hapgraph)
static void	listTaxaForPHG()
static void	main(String[] args)
static int	maxTaxaPerRange(HaplotypeGraph graph)
static com.google.common.collect.Multiset<Integer>	readHapidCounts(String filename)
static Map<Integer,Integer>	readHapidMap(String filename)
static void	storeFastqToHapCountResult()
static void	storeHapidCounts(String filename, com.google.common.collect.Multiset<Integer> hapidCounts)
static void	storeHapidMap(String filename, Map<Integer,Integer> hapidCounts)
static void	testB73W22()
static void	testFastqToHapCount(String name1, String name2)
static void	testReadsPerRange()
static void	twoLineNodeCounts(String line1, String line2, String outfile)
static void	twoLineTest(String name1, String name2)
static void	writeNodeStatistics(HaplotypeGraph graph, List<HaplotypeNode> path, Map<Integer,Integer> inclusionCountMap, Map<Integer,Integer> exclusionCountMap, String target)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

hapidCountFilename

public static String hapidCountFilename

configFileName

public static String configFileName

configFile

public static String configFile

genomeVersionName

public static String genomeVersionName

methodIdName

public static String methodIdName

samFileName

public static String samFileName

readFileName

public static String readFileName

hapidCountMapFileName

public static String hapidCountMapFileName

minTaxaPerRange

public static int minTaxaPerRange

Constructor Detail

ConvertGBSUtils

public ConvertGBSUtils()

Method Detail

main

public static void main(String[] args)

buildHaplotypeGraph

public static HaplotypeGraph buildHaplotypeGraph()

countSeqCharInPHG

public static void countSeqCharInPHG()

writeNodeStatistics

public static void writeNodeStatistics(HaplotypeGraph graph,
                                       List<HaplotypeNode> path,
                                       Map<Integer,Integer> inclusionCountMap,
                                       Map<Integer,Integer> exclusionCountMap,
                                       String target)

maxTaxaPerRange

public static int maxTaxaPerRange(HaplotypeGraph graph)

storeFastqToHapCountResult

public static void storeFastqToHapCountResult()

testFastqToHapCount

public static void testFastqToHapCount(String name1,
                                       String name2)

basicConverterTest

public static void basicConverterTest()

testReadsPerRange

public static void testReadsPerRange()

testB73W22

public static void testB73W22()

twoLineTest

public static void twoLineTest(String name1,
                               String name2)

twoLineNodeCounts

public static void twoLineNodeCounts(String line1,
                                     String line2,
                                     String outfile)

listBadNodes

public static void listBadNodes(String comp,
                                String outfile)

countNodesWithW22

public static void countNodesWithW22(List<HaplotypeNode> myNodes)

countW22NodesFullGraph

public static void countW22NodesFullGraph(HaplotypeGraph hapgraph)

howManyAnchorsHaveW22InMostFrequentNode

public static void howManyAnchorsHaveW22InMostFrequentNode(HaplotypeGraph hapgraph,
                                                           com.google.common.collect.Multiset<Integer> hapidCounts)

containsW22

public static boolean containsW22(net.maizegenetics.taxa.TaxaList taxa)

contains

public static boolean contains(String name,
                               net.maizegenetics.taxa.TaxaList taxa)

chooseBestNode

public List<HaplotypeNode> chooseBestNode(HaplotypeGraph hapgraph,
                                          com.google.common.collect.Multiset<Integer> hapidCounts)

evaluateOneBestNodeRanges

public void evaluateOneBestNodeRanges(HaplotypeGraph hapgraph,
                                      com.google.common.collect.Multiset<Integer> hapidCounts)

listTaxaForPHG

public static void listTaxaForPHG()

listTaxa

public static void listTaxa(HaplotypeGraph hapgraph)

readHapidCounts

public static com.google.common.collect.Multiset<Integer> readHapidCounts(String filename)
                                                                   throws IOException,
                                                                          ClassNotFoundException

Throws:

IOException

ClassNotFoundException

storeHapidCounts

public static void storeHapidCounts(String filename,
                                    com.google.common.collect.Multiset<Integer> hapidCounts)
                             throws IOException

Throws:

IOException

readHapidMap

public static Map<Integer,Integer> readHapidMap(String filename)
                                         throws IOException,
                                                ClassNotFoundException

Throws:

IOException

ClassNotFoundException

storeHapidMap

public static void storeHapidMap(String filename,
                                 Map<Integer,Integer> hapidCounts)
                          throws IOException

Throws:

IOException