net.maizegenetics.pangenome.db_loading

Class DBLoadingUtils

java.lang.Object

net.maizegenetics.pangenome.db_loading.DBLoadingUtils

public class DBLoadingUtils
extends Object

Common methods used by postgres and sqlite dbs for loading/retrieving data from the PHG dbs. This is the place encoding/decoding methods for table data should stored. Authors zrm22 and lcj34.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DBLoadingUtils.AnchorType
static class	DBLoadingUtils.MethodType

Constructor Summary

Constructors

Constructor and Description
DBLoadingUtils()

Method Summary

Modifier and Type	Method and Description
static Connection	connection(String propertiesFile, boolean createNew) Creates a database connection given a properties file It is expected that only initial db loading methods will call this with "createNew" = true.
static Connection	connection(String host, String user, String password, String dbName, String type, boolean createNew) Creates a new database connection or returns connection to existing db If createNew is FALSE then try to connect, and if db doesn't exist, return NULL NOTE: from postgres, User should never create a db that matches all lower case to an existing db.
static List<htsjdk.variant.variantcontext.VariantContext>	decodeByteArrayToListOfVariantContext(byte[] encodedByteArray)
static int[][]	decodeHapCountsArray(byte[] dataAsByteArray)
static int[]	decodePathsArray(byte[] dataAsByteArray)
static byte[]	encodeHapCountsArrayFromFile(String fileName)
static byte[]	encodeHapCountsArrayFromMultiset(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet, com.google.common.collect.Multiset<HaplotypeNode> exclusionHitSet) THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts.
static byte[]	encodePathArrayFromSet(Set<HaplotypeNode> paths)
static byte[]	encodeSelectedVCFRegionsToByteArray(String fileName, boolean onlyVariants, boolean mergeRefRanges, com.google.common.collect.Range<net.maizegenetics.dna.map.Position> interval)
static byte[]	encodeVariantContextListToByteArray(List<htsjdk.variant.variantcontext.VariantContext> listOfVariants, boolean mergeRefRanges)
static byte[]	encodeVariantContextStreamToByteArray(Stream<htsjdk.variant.variantcontext.VariantContext> variantStream, boolean onlyVariants, boolean mergeRefRanges)
static byte[]	encodeVCFFileToByteArray(String fileName, boolean onlyVariants, boolean mergeRefRanges)
static List<String>	splitCigar(String cigarString)
static Set<String>	verifyIntervalRanges(String anchorFile)

Methods inherited from class java.lang.Object

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

Constructor Detail

DBLoadingUtils

public DBLoadingUtils()

Method Detail

connection

public static Connection connection(String propertiesFile,
                                    boolean createNew)

Creates a database connection given a properties file It is expected that only initial db loading methods will call this with "createNew" = true.

Parameters:

propertiesFile - properties file

createNew - Indicates if the request is to connect to an existing db or to create a new one with the specified name.

Returns:

database connection

connection

public static Connection connection(String host,
                                    String user,
                                    String password,
                                    String dbName,
                                    String type,
                                    boolean createNew)

Creates a new database connection or returns connection to existing db If createNew is FALSE then try to connect, and if db doesn't exist, return NULL NOTE: from postgres, User should never create a db that matches all lower case to an existing db. This will cause errors as our db check verifies based on all-lower case. To get a camel-case db name, the db must be created and accessed using This is likely to cause confusion, so this code defaults to postgres all-lowercase db names.

Parameters:

host - hostname

user - user id

password - password

dbName - database name

dbType - database type (sqlite or postgres)

createNew - if true, delete old db if it exists; create new db from PHG schema

Returns:

SQLite database connection

verifyIntervalRanges

public static Set<String> verifyIntervalRanges(String anchorFile)

encodeSelectedVCFRegionsToByteArray

public static byte[] encodeSelectedVCFRegionsToByteArray(String fileName,
                                                         boolean onlyVariants,
                                                         boolean mergeRefRanges,
                                                         com.google.common.collect.Range<net.maizegenetics.dna.map.Position> interval)

encodeVCFFileToByteArray

public static byte[] encodeVCFFileToByteArray(String fileName,
                                              boolean onlyVariants,
                                              boolean mergeRefRanges)

encodeVariantContextStreamToByteArray

public static byte[] encodeVariantContextStreamToByteArray(Stream<htsjdk.variant.variantcontext.VariantContext> variantStream,
                                                           boolean onlyVariants,
                                                           boolean mergeRefRanges)
                                                    throws IOException

Throws:

IOException

encodeVariantContextListToByteArray

public static byte[] encodeVariantContextListToByteArray(List<htsjdk.variant.variantcontext.VariantContext> listOfVariants,
                                                         boolean mergeRefRanges)
                                                  throws IOException

Throws:

IOException

decodeByteArrayToListOfVariantContext

public static List<htsjdk.variant.variantcontext.VariantContext> decodeByteArrayToListOfVariantContext(byte[] encodedByteArray)

encodeHapCountsArrayFromMultiset

public static byte[] encodeHapCountsArrayFromMultiset(com.google.common.collect.Multiset<HaplotypeNode> perfectHitSet,
                                                      com.google.common.collect.Multiset<HaplotypeNode> exclusionHitSet)

THis method takes 2 multisets of HaplotypeNode objects: one indicating inclusion counts for a haplotype, the other indicating exclusion counts. These sets are on a per-taxon basis. The data will be written compressed to a byte array for storage in the PHG db haplotype_counts table. If indicated, the data will also be written to files.

Returns:

encodeHapCountsArrayFromFile

public static byte[] encodeHapCountsArrayFromFile(String fileName)

decodeHapCountsArray

public static int[][] decodeHapCountsArray(byte[] dataAsByteArray)

encodePathArrayFromSet

public static byte[] encodePathArrayFromSet(Set<HaplotypeNode> paths)

decodePathsArray

public static int[] decodePathsArray(byte[] dataAsByteArray)

splitCigar

public static List<String> splitCigar(String cigarString)