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PHG - Practical Haplotype Graph

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SQLite format 3@  ''.@?
?;
?=?
???q?????YtablemethodsmethodsCREATE TABLE methods (
   method_id INTEGER PRIMARY KEY,
   name TEXT UNIQUE,
   description TEXT   
)-Aindexsqlite_autoindex_methods_1methods?//?Wtableanchor_alignmentsanchor_alignmentsCREATE TABLE anchor_alignments (
    anchorid INTEGER PRIMARY KEY,
    method_id INTEGER,
    msa BLOB NOT NULL,
    FOREIGN KEY (anchorid) REFERENCES anchors(anchorid),
    FOREIGN KEY (method_id) REFERENCES methods(method_id)
)?
//?Gtableanchor_haplotypesanchor_haplotypesCREATE TABLE anchor_haplotypes (
    anchor_haplotypes_id INTEGER PRIMARY KEY,
    hapid INTEGER,
    anchorid INTEGER NOT NULL,
    anchor_sequence_id INTEGER,
    method_id INTEGER,
    assembly_chrom TEXT,
    assembly_start INTEGER,
    assembly_end INTEGER,
    additional_data TEXT,
    UNIQUE (hapid, anchorid,anchor_sequence_id, method_id),
    FOREIGN KEY (hapid) REFERENCES haplotypes(hapid),
    FOREIGN KEY (anchorid) REFERENCES anchors(anchorid),
    FOREIGN KEY (anchor_sequence_id) REFERENCES anchor_sequences(anchor_sequence_id),
    FOREIGN KEY (method_id) REFERENCES methods(method_id)
)AU/indexsqlite_autoindex_anchor_haplotypes_1anchor_haplotypes?
!!?_tablehaplotypeshaplotypesCREATE TABLE haplotypes (
    hapid INTEGER PRIMARY KEY,
    genoid INTEGER NOT NULL,
    hapNumber INTEGER NOT NULL,
    phasingConfidence FLOAT,
    UNIQUE (genoid,hapNumber),
    FOREIGN KEY (genoid) REFERENCES genotypes(genoid)
)3G!indexsqlite_autoindex_haplotypes_1haplotypes
?	?qtablegenotypesgenotypes
CREATE TABLE genotypes (
    genoid INTEGER   PRIMARY KEY,
    ploidy INTEGER NOT NULL,
    is_reference BOOLEAN,
    line_name TEXT NOT NULL UNIQUE,
    line_data TEXT,
    isPhasedAcrossGenes BOOLEAN,
    isPhasedAcrossChromosomes BOOLEAN
)1
Eindexsqlite_autoindex_genotypes_1genotypes?Y?tableedgeedge	CREATE TABLE edge (
   edge_id INTEGER PRIMARY KEY,
   anchor_haplotype_id1 INTEGER,
   anchor_haplotype_id2 INTEGER,
   is_id1_anchor BOOLEAN,
   is_id2_anchor BOOLEAN,
   method_id INTEGER,
   quality_score FLOAT,
   FOREIGN KEY (anchor_haplotype_id1) REFERENCES anchor_haployptes(anchor_haplotype_id),
   FOREIGN KEY (anchor_haplotype_id2) REFERENCES anchor_haplotypes(anchor_haplotype_id),
   FOREIGN KEY (method_id) REFERENCES methods(method_id)
)?DGG?tableanchorseq_consensus_anchorseqanchorseq_consensus_anchorseqCREATE TABLE anchorseq_consensus_anchorseq (
   anchor_sequence_id INTEGER,
   consensus_anchor_sequence_id INTEGER,
   PRIMARY KEY(anchor_sequence_id,consensus_anchor_sequence_id),
   FOREIGN KEY (anchor_sequence_id) REFERENCES anchor_sequences(anchor_sequence_id),
   FOREIGN KEY (consensus_anchor_sequence_id) REFERENCES consensus_anchor_sequence(consensus_anchor_sequence_id)
)YmGindexsqlite_autoindex_anchorseq_consensus_anchorseq_1anchorseq_consensus_anchorseq?/???mtableconsensus_anchor_sequenceconsensus_anchor_sequenceCREATE TABLE consensus_anchor_sequence (
   consensus_anchor_sequence_id INTEGER PRIMARY KEY,
   sequence TEXT
)?i--?tableanchor_sequencesanchor_sequencesCREATE TABLE anchor_sequences (
    anchor_sequence_id INTEGER PRIMARY KEY,
    sequence TEXT,
    seq_len int,
    seq_hash TEXT,
    anchor_seq_UUID TEXT,
    UNIQUE (seq_hash,seq_len)
)?S-indexsqlite_autoindex_anchor_sequences_1anchor_sequences?,?/tableanchorsanchorsCREATE TABLE anchors (
    anchorid INTEGER PRIMARY KEY,
    version_id INTEGER,
    chrom	TEXT,   
    anchor_start INTEGER NOT NULL,
    anchor_end INTEGER NOT NULL,
    gene_start INTEGER NOT NULL,
    gene_end INTEGER NOT NULL,
    anchor_UUID TEXT,
    is_anchor BOOLEAN,
    FOREIGN KEY (version_id) REFERENCES anchor_versions(version_id),
    UNIQUE (version_id,chrom,anchor_start,anchor_end)
)-Aindexsqlite_autoindex_anchors_1anchors
???
		10nqopUUID_a_1
		10dgefUUID_a_1
???	10nq
		10dg
??g41MACTAj1f8f4bf413b16ad135722aa4591043eUUID_11MGGCGd940c791b39e86d2f2cdf549aabaa33aUUID_41MACGCedda3af3f92234c237fdc95a6e778273UUID_31MGCTA7a75594ad17303d925bd7c02d9e2d020UUID_21MACGTf1f8f4bf413b16ad135722aa4591043eUUID_1
>?e??>&Mj1f8f4bf413b16ad135722aa4591043e&Md940c791b39e86d2f2cdf549aabaa33a&Medda3af3f92234c237fdc95a6e778273&M7a75594ad17303d925bd7c02d9e2d020%M	f1f8f4bf413b16ad135722aa4591043e
?????ACTAGGCGGCTAACGN
??????			
??????				

????$	%falseCNon_B73_fakefalsefalse$	%falseBNon_B73_fakefalsefalse	trueAB73_fakefalsefalse
????CB	A
????				
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	1

		1
	1

		1

		1
				1
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????
?;
?=?
???q????++?Wtableanchor_versionsanchor_versionsCREATE TABLE anchor_versions (
   version_id INTEGER PRIMARY KEY,
   name TEXT,
   description TEXT
)??YtablemethodsmethodsCREATE TABLE methods (
   method_id INTEGER PRIMARY KEY,
   name TEXT UNIQUE,
   description TEXT   
)-Aindexsqlite_autoindex_methods_1methods?//?Wtableanchor_alignmentsanchor_alignmentsCREATE TABLE anchor_alignments (
    anchorid INTEGER PRIMARY KEY,
    method_id INTEGER,
    msa BLOB NOT NULL,
    FOREIGN KEY (anchorid) REFERENCES anchors(anchorid),
    FOREIGN KEY (method_id) REFERENCES methods(method_id)
)?
//?Gtableanchor_haplotypesanchor_haplotypesCREATE TABLE anchor_haplotypes (
    anchor_haplotypes_id INTEGER PRIMARY KEY,
    hapid INTEGER,
    anchorid INTEGER NOT NULL,
    anchor_sequence_id INTEGER,
    method_id INTEGER,
    assembly_chrom TEXT,
    assembly_start INTEGER,
    assembly_end INTEGER,
    additional_data TEXT,
    UNIQUE (hapid, anchorid,anchor_sequence_id, method_id),
    FOREIGN KEY (hapid) REFERENCES haplotypes(hapid),
    FOREIGN KEY (anchorid) REFERENCES anchors(anchorid),
    FOREIGN KEY (anchor_sequence_id) REFERENCES anchor_sequences(anchor_sequence_id),
    FOREIGN KEY (method_id) REFERENCES methods(method_id)
)AU/indexsqlite_autoindex_anchor_haplotypes_1anchor_haplotypes?
!!?_tablehaplotypeshaplotypesCREATE TABLE haplotypes (
    hapid INTEGER PRIMARY KEY,
    genoid INTEGER NOT NULL,
    hapNumber INTEGER NOT NULL,
    phasingConfidence FLOAT,
    UNIQUE (genoid,hapNumber),
    FOREIGN KEY (genoid) REFERENCES genotypes(genoid)
)3G!indexsqlite_autoindex_haplotypes_1haplotypes
?	?qtablegenotypesgenotypes
CREATE TABLE genotypes (
    genoid INTEGER   PRIMARY KEY,
    ploidy INTEGER NOT NULL,
    is_reference BOOLEAN,
    line_name TEXT NOT NULL UNIQUE,
    line_data TEXT,
    isPhasedAcrossGenes BOOLEAN,
    isPhasedAcrossChromosomes BOOLEAN
)1
Eindexsqlite_autoindex_genotypes_1genotypes?Y?tableedgeedge	CREATE TABLE edge (
   edge_id INTEGER PRIMARY KEY,
   anchor_haplotype_id1 INTEGER,
   anchor_haplotype_id2 INTEGER,
   is_id1_anchor BOOLEAN,
   is_id2_anchor BOOLEAN,
   method_id INTEGER,
   quality_score FLOAT,
   FOREIGN KEY (anchor_haplotype_id1) REFERENCES anchor_haployptes(anchor_haplotype_id),
   FOREIGN KEY (anchor_haplotype_id2) REFERENCES anchor_haplotypes(anchor_haplotype_id),
   FOREIGN KEY (method_id) REFERENCES methods(method_id)
)?DGG?tableanchorseq_consensus_anchorseqanchorseq_consensus_anchorseqCREATE TABLE anchorseq_consensus_anchorseq (
   anchor_sequence_id INTEGER,
   consensus_anchor_sequence_id INTEGER,
   PRIMARY KEY(anchor_sequence_id,consensus_anchor_sequence_id),
   FOREIGN KEY (anchor_sequence_id) REFERENCES anchor_sequences(anchor_sequence_id),
   FOREIGN KEY (consensus_anchor_sequence_id) REFERENCES consensus_anchor_sequence(consensus_anchor_sequence_id)
)YmGindexsqlite_autoindex_anchorseq_consensus_anchorseq_1anchorseq_consensus_anchorseq?/???mtableconsensus_anchor_sequenceconsensus_anchor_sequenceCREATE TABLE consensus_anchor_sequence (
   consensus_anchor_sequence_id INTEGER PRIMARY KEY,
   sequence TEXT
)?i--?tableanchor_sequencesanchor_sequencesCREATE TABLE anchor_sequences (
    anchor_sequence_id INTEGER PRIMARY KEY,
    sequence TEXT,
    seq_len int,
    seq_hash TEXT,
    anchor_seq_UUID TEXT,
    UNIQUE (seq_hash,seq_len)
)?S-indexsqlite_autoindex_anchor_sequences_1anchor_sequences?,?/tableanchorsanchorsCREATE TABLE anchors (
    anchorid INTEGER PRIMARY KEY,
    version_id INTEGER,
    chrom	TEXT,   
    anchor_start INTEGER NOT NULL,
    anchor_end INTEGER NOT NULL,
    gene_start INTEGER NOT NULL,
    gene_end INTEGER NOT NULL,
    anchor_UUID TEXT,
    is_anchor BOOLEAN,
    FOREIGN KEY (version_id) REFERENCES anchor_versions(version_id),
    UNIQUE (version_id,chrom,anchor_start,anchor_end)
)-Aindexsqlite_autoindex_anchors_1anchors




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