assembly_pipeline Struct Reference

Detailed description

HaplotypeCaller Pipeline Structures

Definition at line 41 of file haplotype_caller.h.

#include <haplotype_caller.h>

Public Methods
void	load_ref (io::SequenceDataHost &h_ref)
void	prep_assembly_sequences (const io::SequenceDataHost &h_ref, const BAM_alignment_batch_SoA &read_batch, const H_VectorActiveRegions active_regions)

Public Members
io::SequenceDataDevice	d_ref
RefSequenceSet	d_ref_seqs
D_VectorU32	d_active_region_ids
D_VectorU32	d_active_region_offsets
D_SequenceSet	d_seq_set
D_VectorDNA	d_set_seqs_data
D_VectorU64	d_set_offsets

Static Public Members
static const uint32	kmer_size = 10
static const uint32	k_best_haplotypes = 12
static const uint32	active_region_size = 100
static const bool	increaze_kmer_size_for_cycles = false
static const uint32	max_reads_in_region_per_sample = 1000
static const uint32	min_reads_per_alignment_start = 5
static const uint32	max_ref_size = 1000
static const uint32	ref_padding = 100

Member Function Documentation

void assembly_pipeline::load_ref ( io::SequenceDataHost &  h_ref)

inline

Definition at line 75 of file haplotype_caller.h.

void assembly_pipeline::prep_assembly_sequences ( const io::SequenceDataHost &  h_ref, const BAM_alignment_batch_SoA &  read_batch, const H_VectorActiveRegions  active_regions  )

inline

Definition at line 81 of file haplotype_caller.h.

Member Data Documentation

const uint32 assembly_pipeline::active_region_size = 100

static

Definition at line 47 of file haplotype_caller.h.

D_VectorU32 assembly_pipeline::d_active_region_ids

Definition at line 61 of file haplotype_caller.h.

D_VectorU32 assembly_pipeline::d_active_region_offsets

Definition at line 62 of file haplotype_caller.h.

io::SequenceDataDevice assembly_pipeline::d_ref

Definition at line 57 of file haplotype_caller.h.

RefSequenceSet assembly_pipeline::d_ref_seqs

Definition at line 58 of file haplotype_caller.h.

D_SequenceSet assembly_pipeline::d_seq_set

Definition at line 65 of file haplotype_caller.h.

D_VectorU64 assembly_pipeline::d_set_offsets

Definition at line 67 of file haplotype_caller.h.

D_VectorDNA assembly_pipeline::d_set_seqs_data

Definition at line 66 of file haplotype_caller.h.

const bool assembly_pipeline::increaze_kmer_size_for_cycles = false

static

Definition at line 48 of file haplotype_caller.h.

const uint32 assembly_pipeline::k_best_haplotypes = 12

static

Definition at line 46 of file haplotype_caller.h.

const uint32 assembly_pipeline::kmer_size = 10

static

Definition at line 45 of file haplotype_caller.h.

const uint32 assembly_pipeline::max_reads_in_region_per_sample = 1000

static

Definition at line 49 of file haplotype_caller.h.

const uint32 assembly_pipeline::max_ref_size = 1000

static

Definition at line 51 of file haplotype_caller.h.

const uint32 assembly_pipeline::min_reads_per_alignment_start = 5

static

Definition at line 50 of file haplotype_caller.h.

const uint32 assembly_pipeline::ref_padding = 100

static

Definition at line 52 of file haplotype_caller.h.

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvMicroAssembly/haplotype_caller.h