ivc

May 14, 2016

Changes in this version

+ var MUT = &sync.Mutex

+ func AlignCostVarLoci(read, ref, qual []byte, prob float64) float64

+ func InitTraceKMat(arr_len int) [][][]byte

Jan 6, 2016

Changes in this version

+ var PARA *ParaInfo

+ var PRINT_MEMSTATS = false

+ var UNALIGN_READ_INFO = make([]*UnAlnReadInfo, 0)

+ func GetVarProfInfo(file_name string) map[string]map[int]VarProfInfo

+ type UnAlnReadInfo struct

+ type VarCallIndex struct

+ ChrName [][]byte

+ ChrPos []int

+ DelVar map[int]int

+ RevFMI *fmi.Index

+ SameLenVar map[int]int

+ Seq []byte

+ SeqLen int

+ VarAF map[int][]float32

+ Variants map[int][][]byte

+ func (VC *VarCallIndex) CallVariants()

+ func (VC *VarCallIndex) ExtendSeeds(s_pos, e_pos, m_pos int, read, qual []byte, edit_aln_info *EditAlnInfo) ([]*VarInfo, int, int, float64)

+ func (VC *VarCallIndex) ForwardSearchFrom(pattern []byte, s_pos int) (int, int, int)

+ func (VC *VarCallIndex) LeftAlign(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCallIndex) LeftAlignEditTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

+ func (VC *VarCallIndex) OutputVarCalls()

+ func (VC *VarCallIndex) ReadReads(read_data chan *ReadInfo, read_signal chan bool)

+ func (VC *VarCallIndex) RightAlign(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCallIndex) RightAlignEditTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

+ func (VC *VarCallIndex) SearchSeeds(read []byte, s_pos int, m_pos []int) (int, int, int, bool)

+ func (VC *VarCallIndex) SearchSeedsPE(read_info *ReadInfo, seed_pos [][]int, rand_gen *rand.Rand) (*SeedInfo, *SeedInfo, bool)

+ func (VC *VarCallIndex) SearchVariants(read_data chan *ReadInfo, read_signal chan bool, var_info []chan *VarInfo, ...)

+ func (VC *VarCallIndex) SearchVariantsPE(read_info *ReadInfo, edit_aln_info *EditAlnInfo, seed_pos [][]int, ...)

+ func (VC *VarCallIndex) UpdateVariantProb(var_info *VarInfo)

type VarProf

+ AlnProb map[uint32]map[string][]float64

+ ChrDiff map[uint32]map[string][]int

+ ChrDis map[uint32]map[string][]int

+ ChrProb map[uint32]map[string][]float64

+ MapProb map[uint32]map[string][]float64

+ ReadInfo map[uint32]map[string][][]byte

+ StartPos1 map[uint32]map[string][]int

+ StartPos2 map[uint32]map[string][]int

+ Strand1 map[uint32]map[string][]bool

+ Strand2 map[uint32]map[string][]bool

+ VarBQual map[uint32]map[string][][]byte

+ VarProb map[uint32]map[string]float64

+ VarRNum map[uint32]map[string]int

+ VarType map[uint32]map[string]int

+ type VarProfInfo struct

+ AleFreq []float32

+ Variant [][]byte

Nov 19, 2015

Changes in this version

+ func GetGenome(file_name string) (chr_pos []int, chr_name [][]byte, seq []byte)

+ func GetSeq(seq []byte)

+ func GetVarProf(file_name string) map[string]map[int]VarProf

type MultiGenome

+ ChrName [][]byte

+ ChrPos []int

+ func (MG *MultiGenome) SearchSeeds(read, rev_read []byte, p int, m_pos []int) (int, int, int, bool)

+ func (MG *MultiGenome) SearchSeedsPE(read_info *ReadInfo, seed_pos [][]int, rand_gen *rand.Rand) (*SeedInfo, *SeedInfo, bool)

type VarCall

+ func (VC *VarCall) SearchVariants(read_data chan *ReadInfo, read_signal chan bool, var_results chan *VarInfo, ...)

+ func (VC *VarCall) SearchVariantsPE(read_info *ReadInfo, edit_aln_info *EditAlnInfo, seed_pos [][]int, ...)

Nov 6, 2015

Changes in this version

+ var SEQ []byte

+ func ReadSequence(file string)

+ type FMIndex struct

+ C map[byte]uint32

+ END_POS uint32

+ EP map[byte]uint32

+ Freq map[byte]uint32

+ LEN uint32

+ OCC map[byte][]uint32

+ SA []uint32

+ SYMBOLS []int

+ func Load(dir string) *FMIndex

+ func NewFMIndex(file string) *FMIndex

+ func (I *FMIndex) Save(file string)

type MultiGenome

+ Header []byte

+ type Symb_OCC struct

+ OCC []uint32

+ Symb int

Sep 13, 2015

Changes in this version

+ var P_AB map[string]float64

+ var VAR_TRACE_INFO_MAP = make(map[uint32][]Var_trace_info)

type EditAlnInfo

+ Bw_Dist_D [][]float64

+ Bw_Dist_IS [][]float64

+ Bw_Dist_IT [][]float64

+ Bw_Trace_D [][][]int

+ Bw_Trace_IS [][][]int

+ Bw_Trace_IT [][][]int

+ Fw_Dist_D [][]float64

+ Fw_Dist_IS [][]float64

+ Fw_Dist_IT [][]float64

+ Fw_Trace_D [][][]int

+ Fw_Trace_IS [][][]int

+ Fw_Trace_IT [][][]int

type Index

+ DelVar map[int]int

+ RevFMI fmi.Index

+ SameLenVar map[int]int

+ Seq []byte

+ VarAF map[int][]float32

+ VarProf map[int][][]byte

+ func NewIndex() *Index

+ func (I *Index) FindSeedsPE(read_info *ReadInfo, seed_pos [][]int, rand_gen *rand.Rand) (*SeedInfo, *SeedInfo, bool)

type InputInfo

+ Cpu_prof_file string

+ Mem_prof_file string

+ Prob_thres float64

+ Ref_file string

+ Var_call_file string

+ Var_prof_file string

type VarCall

+ func (VC *VarCall) BackwardDistance(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) BackwardTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) ForwardDistance(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) ForwardTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

type VarInfo

+ CProb float64

+ type Var_trace_info struct

Oct 8, 2015

Changes in this version

+ var CPU_FILE *os.File

+ var GET_UNALIGN_INFO = true

+ var INDEL_ERR_RATE = 0.0000001

+ var L2E []float64

+ var MEM_FILE *os.File

+ var MULTI_GENOME *MultiGenome

+ var PRINT_UNALIGN_INFO = false

+ var PRINT_VAR_CALL_INFO = false

+ var Q2C map[byte]float64

+ var Q2E map[byte]float64

+ var Q2P map[byte]float64

+ var UNALIGN_INFO_ARR = make([]UnAlignInfo, 0)

+ var UNALIGN_INFO_CHAN = make(chan UnAlignInfo)

+ func BuildMultiGenome(genome_file, var_prof_file string) ([]byte, map[int]VarProf)

+ func InitEditAlnMat(arr_len int) ([][]float64, [][][]int)

+ func IntervalHasVariants(A []int, i, j int) bool

+ func LoadMultiSeq(file_name string) []byte

+ func LoadVarProf(file_name string) (map[int][][]byte, map[int][]float32)

+ func PrintGetVariants(mess string, paired_prob, prob1, prob2 float64, vars1, vars2 []*VarInfo)

+ func PrintRefPosMap(l_ref_pos_map, r_ref_pos_map []int)

+ func SaveMultiSeq(file_name string, multi_seq []byte)

+ func SaveVarProf(file_name string, var_prof map[int]VarProf)

+ func Setup(input_para_info *ParaInfo)

+ type EditAlnInfo struct

+ func InitEditAlnInfo(arr_len int) *EditAlnInfo

+ type MultiGenome struct

+ DelVar map[int]int

+ RevFMI fmi.Index

+ SameLenVar map[int]int

+ Seq []byte

+ VarAF map[int][]float32

+ Variants map[int][][]byte

+ func NewMultiGenome() *MultiGenome

+ func (MG *MultiGenome) BackwardSearchFrom(pattern []byte, start_pos int) (int, int, int)

+ func (MG *MultiGenome) FindSeeds(read, rev_read []byte, p int, m_pos []int) (int, int, int, bool)

+ func (MG *MultiGenome) FindSeedsPE(read_info *ReadInfo, seed_pos [][]int, rand_gen *rand.Rand) (*SeedInfo, *SeedInfo, bool)

type ParaInfo

+ Debug_mode bool

+ Gap_ext float64

+ Gap_open float64

+ Index_file string

+ Max_psnum int

+ Max_slen int

+ Max_snum int

+ Min_slen int

+ Proc_num int

+ Read_file_1 string

+ Read_file_2 string

+ Ref_file string

+ Rev_index_file string

+ Search_mode int

+ Search_step int

+ Start_pos int

+ Var_call_file string

+ Var_prof_file string

+ func SetupPara(input_para_info *ParaInfo) *ParaInfo

+ type SeedInfo struct

+ type UnAlignInfo struct

+ type UnAlnInfo struct

+ type VarCall struct

+ AlnProb map[uint32]map[string][]float64

+ ChrDiff map[uint32]map[string][]int

+ ChrDis map[uint32]map[string][]int

+ ChrProb map[uint32]map[string][]float64

+ MapProb map[uint32]map[string][]float64

+ ReadInfo map[uint32]map[string][][]byte

+ StartPos1 map[uint32]map[string][]int

+ StartPos2 map[uint32]map[string][]int

+ Strand1 map[uint32]map[string][]bool

+ Strand2 map[uint32]map[string][]bool

+ VarBQual map[uint32]map[string][][]byte

+ VarProb map[uint32]map[string]float64

+ VarRNum map[uint32]map[string]int

+ VarType map[uint32]map[string]int

+ func NewVariantCaller() *VarCall

+ func (VC *VarCall) CallVariants()

+ func (VC *VarCall) ExtendSeeds(s_pos, e_pos, m_pos int, read, qual []byte, edit_aln_info *EditAlnInfo) ([]*VarInfo, int, int, float64)

+ func (VC *VarCall) FindVariants(read_data chan *ReadInfo, read_signal chan bool, var_results chan *VarInfo, ...)

+ func (VC *VarCall) FindVariantsPE(read_info *ReadInfo, edit_aln_info *EditAlnInfo, seed_pos [][]int, ...)

+ func (VC *VarCall) LeftAlign(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) LeftAlignEditTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) OutputVarCalls()

+ func (VC *VarCall) ReadReads(read_data chan *ReadInfo, read_signal chan bool)

+ func (VC *VarCall) RightAlign(read, qual, ref []byte, pos int, D, IS, IT [][]float64, ...) (float64, float64, int, int, int, []int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) RightAlignEditTraceBack(read, qual, ref []byte, m, n int, pos int, BT_Mat int, ...) ([]int, [][]byte, [][]byte, []int)

+ func (VC *VarCall) UpdateVariantProb(var_info *VarInfo)

+ type VarInfo struct

+ AProb float64

+ BQual []byte

+ Bases []byte

+ CDiff int

+ CDis int

+ IProb float64

+ MProb float64

+ Pos uint32

+ RInfo []byte

+ SPos1 int

+ SPos2 int

+ Strand1 bool

+ Strand2 bool

+ Type int

+ type VarProf struct

+ AleFreq []float32

+ Variant [][]byte

Jul 10, 2015

Changes in this version

+ var PRINT_EDIT_DIST_MAT_INFO = false

+ func AlignCostKnownLoci(read, ref, qual []byte, prob float64) float64

+ func GetEditTrace(mess string, i, j int, read, ref byte)

+ func GetEditTraceKnownLoc(mess string, i, j int, read []byte, ref byte)

+ func PrintComparedReadRef(read_l_flank, ref_l_flank, read_r_flank, ref_r_flank []byte)

+ func PrintDisInfo(mess string, i, j int, d float64)

+ func PrintGetSNP(p_prob, m_prob1, m_prob2 float64, snps1, snps2 []SNP)

+ func PrintVarInfo(mess string, snp_pos []int, snp_val, snp_qlt [][]byte)

type AlignInfo

+ Bw_Dist_D [][]float64

+ Bw_Dist_IS [][]float64

+ Bw_Dist_IT [][]float64

+ Bw_Trace_D [][][]int

+ Bw_Trace_IS [][][]int

+ Bw_Trace_IT [][][]int

+ Fw_Dist_D [][]float64

+ Fw_Dist_IS [][]float64

+ Fw_Dist_IT [][]float64

+ Fw_Trace_D [][][]int

+ Fw_Trace_IS [][][]int

+ Fw_Trace_IT [][][]int

type Index

+ func New_Index() *Index

type ParaInfo

+ Gap_ext_cost float64

+ Gap_open_cost float64

+ Ham_backup int

+ Indel_backup int

+ Seed_backup int

+ Sub_cost float64

type SNP

+ SPos1 int

+ SPos2 int

+ Type int

type SNP_Prof

+ SNP_Prob map[uint32]map[string]float64

+ SNP_RNum map[uint32]map[string]int

+ SNP_Type map[uint32]map[string][]int

+ Start_Pos1 map[uint32]map[string][]int

+ Start_Pos2 map[uint32]map[string][]int

+ func New_SNP_Caller(input_info InputInfo) *SNP_Prof

+ func (S *SNP_Prof) FindSNPsFromPairedEnds(read_info *ReadInfo, snp_results chan SNP, align_info *AlignInfo, m_pos []int)

Jul 10, 2015

Changes in this version

+ var NEW_INDEL_RATE = 0.000001

+ var NEW_INDEL_RATE_LOG = -math.Log10(NEW_INDEL_RATE)

+ var NEW_SNP_RATE = 0.00001

+ var NEW_SNP_RATE_LOG = -math.Log10(NEW_SNP_RATE)

+ var PRINT_EDIT_DIST_INFO = false

+ func PrintEditAlignInfo(mess string, read, qual, ref []byte)

+ func PrintEditDisInfo(mess string, i, j int, d float64)

+ func PrintEditDisInput(mess string, str_val ...[]byte)

+ func PrintEditDisMat(mess string, D [][]float64, m, n int)

+ func PrintEditTraceDirection(mess string, i, j int, d1, d2 float64)

+ func PrintEditTraceMat(mess string, BT [][][]int, m, n int)

+ func PrintEditTraceStep(mess string, i, j int, read, ref byte)

+ func PrintEditTraceStepKnownLoc(mess string, i, j int, read []byte, ref byte)

type InputInfo

+ Dist_thres int

+ Iter_num int

Mar 5, 2015

Changes in this version

type SNP_Prof

+ SNP_BaseQ map[uint32]map[string][][]byte

Feb 22, 2015

Changes in this version

type InputInfo

+ Max_slen int

type SNP

+ EPos1 int

+ EPos2 int

+ RInfo []byte

+ Stra1 bool

+ Stra2 bool

type SNP_Prof

+ End_Pos1 map[uint32]map[string][]int

+ End_Pos2 map[uint32]map[string][]int

+ Read_Info map[uint32]map[string][][]byte

+ Strand1 map[uint32]map[string][]bool

+ Strand2 map[uint32]map[string][]bool

Jan 26, 2015

Changes in this version

+ func AlignProb(read, ref, qual []byte, prob float64) float64

type ParaInfo

+ Prob_thres float64

type SNP_Prof

+ func (S *SNP_Prof) BackwardDistance(read, qual, ref []byte, pos int, D [][]float64, T [][][]byte) (float64, float64, int, int, []int, [][]byte, []int)

+ func (S *SNP_Prof) BackwardTraceBack(read, qual, ref []byte, m, n int, pos int, T [][][]byte) ([]int, [][]byte, []int)

+ func (S *SNP_Prof) FindExtensions(read, qual []byte, s_pos, e_pos int, m_pos int, align_info *AlignInfo) (float64, []int, [][]byte, []int, []int, [][]byte, []int, int, int, bool)

+ func (S *SNP_Prof) ForwardDistance(read, qual, ref []byte, pos int, D [][]float64, T [][][]byte) (float64, float64, int, int, []int, [][]byte, []int)

+ func (S *SNP_Prof) ForwardTraceBack(read, qual, ref []byte, m, n int, pos int, T [][][]byte) ([]int, [][]byte, []int)

Jan 5, 2015

Changes in this version

type SNP

+ ADis int

+ AProb float64

+ CDiff int

+ CDis int

+ CProb float64

+ RID []byte

type SNP_Prof

+ Aln_Dis map[uint32]map[string][]int

+ Aln_Prob map[uint32]map[string][]float64

+ Chr_Diff map[uint32]map[string][]int

+ Chr_Dis map[uint32]map[string][]int

+ Chr_Prob map[uint32]map[string][]float64

+ Read_ID map[uint32]map[string][][]byte

Dec 19, 2014

Changes in this version

+ var ALIGN_READ_INFO_ARR = make([]Align_trace_info, 0)

+ var ALIGN_READ_INFO_CHAN = make(chan Align_trace_info)

+ var GET_ALIGN_READ_INFO = true

+ var GET_NO_ALIGN_READ_INFO = true

+ var NO_ALIGN_READ_INFO_ARR = make([]Align_trace_info, 0)

+ var NO_ALIGN_READ_INFO_CHAN = make(chan Align_trace_info)

+ func GetAlignReadInfo()

+ func GetNoAlignReadInfo()

+ func OutputFNSNPInfo(files []*os.File, FN_Pos []int, FN_Var map[int][]byte)

+ func OutputTPFPSNPInfo(files []*os.File, st SNP_trace_info, snp_pos uint32)

+ func PrintPairedSeedInfo(mess string, match_pos_r1, match_pos_r2 int)

+ func ProcessFNSNPInfo(snp_call map[uint32]map[string]float64)

+ func ProcessNoAlignReadInfo(snp_call map[uint32]map[string]float64)

+ func ProcessTPFPSNPInfo(snp_call map[uint32]map[string]float64)

+ func WriteFNSNPInfo(file *os.File, at Align_trace_info, pos int, true_var []byte, ...)

+ func WriteTPFPSNPInfo(file *os.File, st SNP_trace_info, snp_pos uint32, true_var []byte)

type InputInfo

+ Max_psnum int

+ Max_snum int

+ Min_slen int

type ParaInfo

+ Err_rate float32

+ Max_ins int

+ Mut_rate float32

+ Mut_var_factor int

type SNP_Prof

+ func (S *SNP_Prof) FindSNPsFromExtension(s_pos, e_pos, m_pos int, read, qual []byte, align_info *AlignInfo) ([]SNP, int, int, int)

+ func (S *SNP_Prof) FindSeedsFromPairedEnds(read_info *ReadInfo) ([]int, []int, []int, []int, []int, []int, []bool, []bool)

Dec 1, 2014

Changes in this version

+ var ALIGN_TRACE_INFO_ARR = make([]Align_trace_info, 0)

+ var ALIGN_TRACE_INFO_CHAN = make(chan Align_trace_info)

+ var FN_VAR_CALL = make(map[int]SNP_CALL)

+ var FN_VAR_COMP = make(map[int][]byte)

+ var FN_VAR_NONE = make(map[int][]byte)

+ var FN_VAR_PART = make(map[int][]byte)

+ var GET_ALIGN_TRACE_INFO = true

+ var GET_NO_ALIGN_TRACE_INFO = true

+ var MEM_STATS = new(runtime.MemStats)

+ var NO_ALIGN_TRACE_INFO_ARR = make([]Align_trace_info, 0)

+ var NO_ALIGN_TRACE_INFO_CHAN = make(chan Align_trace_info)

+ var PRINT_ALIGN_TRACE_INFO = true

+ var PRINT_FN = true

+ var PRINT_MEM_STATS = false

+ var PRINT_NA = true

+ var PRINT_PROCESS_MEM = true

+ var PRINT_TPFP = true

+ var QUAL_THRES = 25.0

+ var SNP_TRACE_INFO_MAP = make(map[uint32][]SNP_trace_info)

+ var TPFP_VAR_CALL = make(map[int]bool)

+ var TRUE_VAR_COMP = LoadTrueVar("/data/nsvo/test-data/GRCh37_chr1/refs/mutate-0.3300/variant_comp.txt")

+ var TRUE_VAR_NONE = LoadTrueVar("/data/nsvo/test-data/GRCh37_chr1/refs/mutate-0.3300/variant_none.txt")

+ var TRUE_VAR_PART = LoadTrueVar("/data/nsvo/test-data/GRCh37_chr1/refs/mutate-0.3300/variant_part.txt")

+ func GetAlignTraceInfo()

+ func GetNoAlignTraceInfo()

+ func InitAlignMatrix(arr_len int) ([][]int, [][][]byte)

+ func LoadTrueVar(file_name string) map[int][]byte

+ func OutputSNPFNInfo(files []*os.File, FN_Pos []int, FN_Var map[int][]byte)

+ func OutputSNPTPFPInfo(files []*os.File, st SNP_trace_info, snp_pos uint32)

+ func PrintExtendTraceInfo(mess string, match []byte, e_pos, s_pos, match_num int, match_pos []int)

+ func PrintLoopTraceInfo(loop_num int, read []byte)

+ func PrintMatchTraceInfo(i, pos, dis, left_most_pos int, left_snp_pos []int, read []byte)

+ func PrintProcessMem(mesg string)

+ func PrintSeedTraceInfo(mess string, e_pos, s_pos int, read []byte)

+ func ProcessNoAlignInfo(snp_call map[uint32]map[string]float64)

+ func ProcessSNPFNInfo(snp_call map[uint32]map[string]float64)

+ func ProcessSNPTPFPInfo(snp_call map[uint32]map[string]float64)

+ func WriteNoALignInfo(file *os.File, at Align_trace_info)

+ func WriteSNPFNInfo(file *os.File, at Align_trace_info, pos int, true_var []byte, ...)

+ func WriteSNPTPFPInfo(file *os.File, st SNP_trace_info, snp_pos uint32, true_var []byte)

type AlignInfo

+ func InitAlignInfo(arr_len int) *AlignInfo

+ type Align_trace_info struct

type ParaInfo

+ Info_len int

+ Max_diff int

type ReadInfo

+ Info1 []byte

+ Info2 []byte

+ Rev_qual1 []byte

+ Rev_qual2 []byte

+ func InitReadInfo(read_len, info_len int) *ReadInfo

+ type SNP_CALL struct

+ Bases string

+ Prob float64

type SNP_Prof

+ SNP_Bases map[uint32]map[string]int

+ type SNP_trace_info struct

Sep 28, 2014

Changes in this version

+ var STD_BASES = []byte

Sep 15, 2014

Changes in this version

+ var EPSILON float64 = 0.0000000001

+ var INPUT_INFO InputInfo

+ var Memstats = new(runtime.MemStats)

+ var PARA_INFO ParaInfo

+ func PrintMemStats(mesg string)

+ func ProbtoQual(p float64) float32

+ func QualtoProb(e byte) float64

type ParaInfo

+ func SetPara(read_len int, seq_err float32) ParaInfo

type ReadInfo

+ Qual1 []byte

+ Qual2 []byte

+ func (read_info *ReadInfo) PrintReads()

type SNP

+ BaseQ []byte

+ Bases []byte

+ Pos uint32

+ type SNP_Prof struct

+ SNP_Calls map[uint32]map[string]float64

+ SNP_Pos map[uint32]bool

+ func (S *SNP_Prof) CallSNPs() (int, int)

+ func (S *SNP_Prof) FindSNPs(read_data chan ReadInfo, read_signal chan bool, snp_results chan SNP, ...)

+ func (S *SNP_Prof) FindSNPsFromEachEnd(read, rev_read, rev_comp_read, comp_read, qual []byte, align_info *AlignInfo, ...) []SNP

+ func (S *SNP_Prof) FindSNPsFromMatch(read, qual []byte, s_pos, e_pos int, match_pos []int, match_num int, ...) []SNP

+ func (S *SNP_Prof) FindSNPsFromReads(read_info *ReadInfo, snp_results chan SNP, align_info *AlignInfo, ...)

+ func (S *SNP_Prof) Init(input_info InputInfo)

+ func (S *SNP_Prof) OutputSNPCalls()

+ func (S *SNP_Prof) ReadReads(read_data chan ReadInfo, read_signal chan bool)

+ func (S *SNP_Prof) UpdateIndelProb(snp SNP)

+ func (S *SNP_Prof) UpdateSNPProb(snp SNP)

Aug 13, 2014

Changes in this version

+ func IndexN(s, sep []byte, n int) int

+ func SplitN(s, sep []byte, n int) ([][]byte, int)

Aug 7, 2014

Changes in this version

+ type AlignInfo struct

+ Bw_Dis [][]int

+ Bw_Trace [][][]byte

+ Fw_Dis [][]int

+ Fw_Trace [][][]byte

+ func (align_info *AlignInfo) InitAlignInfo(arr_len int)

+ type CalledSNP struct

+ SNPCall []byte

+ SNPPos int

+ SNPProb []int

type InputInfo

+ Proc_num int

+ Routine_num int

type ParaInfo

+ Read_len int

+ Seq_err float32

type ReadInfo

+ Read_info_1 []byte

+ Read_info_2 []byte

+ func (read_info *ReadInfo) AssignReads(read1, read2 []byte)

+ func (read_info *ReadInfo) CalcRevComp()

Jul 28, 2014

Changes in this version

+ var EMPTY_INT_SLICE []int = make([]int, 0)

+ var INDEX Index

+ var RAND_GEN *rand.Rand

+ var SEARCH_MODE int

+ var SEARCH_STEP int

+ var START_POS int

+ func InitMatrix(arr_len int, D *[][]int, T *[][][]byte)

+ func RevComp(read []byte, rev_read, rev_comp_read, comp_read []byte)

+ type AlignMem struct

+ Bw_D [][]int

+ Bw_T [][][]byte

+ Fw_D [][]int

+ Fw_T [][][]byte

+ func (align_mem *AlignMem) AllocMem(arr_len int)

type Index

+ SNP_PROF map[int][][]byte

+ func (I *Index) BackwardDistance(read, ref []byte, pos int, D [][]int, T [][][]byte) (int, int, int, int, []int, [][]byte)

+ func (I *Index) ForwardDistance(read, ref []byte, pos int, D [][]int, T [][][]byte) (int, int, int, int, []int, [][]byte)

+ type InputInfo struct

+ Genome_file string

+ Index_file string

+ Read_file_1 string

+ Read_file_2 string

+ Rev_index_file string

+ SNP_call_file string

+ SNP_file string

+ Search_mode int

+ Search_step int

+ Start_pos int

+ type ParaInfo struct

+ Dist_thres int

+ Err_var_factor int

+ Iter_num int

+ Iter_num_factor int

+ Max_match int

+ type ReadInfo struct

+ Comp_read1 []byte

+ Comp_read2 []byte

+ Qual_info_1 []byte

+ Qual_info_2 []byte

+ Read1 []byte

+ Read2 []byte

+ Read_len int

+ Rev_comp_read1 []byte

+ Rev_comp_read2 []byte

+ Rev_read1 []byte

+ Rev_read2 []byte

+ Seq_err float32

+ func (read_info *ReadInfo) AllocMem() bool

type SNP

+ SNP_Idx int

+ SNP_Val []byte

type SNPProf

+ func (S *SNPProf) FindSNP(read_info ReadInfo, align_mem AlignMem, match_pos []int) []SNP

+ func (S *SNPProf) FindSNPFromMatch(read []byte, s_pos, e_pos int, match_pos []int, match_num int, ...) []SNP

+ type SNPProfile struct

+ AlleleFreq []float32

+ Profile []string

Jun 17, 2014

Changes in this version

type Index

+ SNP_AF map[int][]float32

type SNP

+ AlleleFreq []float32

+ Profile []string

type SNPProf

+ SNP_Conf map[int][]float32

Jun 12, 2014

Changes in this version

+ var INF int = math.MaxInt16

+ func BuildMultigenome(SNP_arr map[int]SNP, seq []byte) []byte

+ func Cost(s, t []byte) int

+ func LoadMultigenome(file_name string) []byte

+ func LoadSNPLocation(file_name string) (map[int][][]byte, map[int]int)

+ func ReadFASTA(sequence_file string) []byte

+ func ReadVCF(sequence_file string) map[int]SNP

+ func ReverseComplement(read []byte) []byte

+ func SaveMultigenome(file_name string, multi []byte)

+ func SaveSNPLocation(file_name string, SNP_arr map[int]SNP)

+ type Index struct

+ FMI fmi.Index

+ REV_FMI fmi.Index

+ SAME_LEN_SNP map[int]int

+ SEQ []byte

+ SNP_PROFILE map[int][][]byte

+ SORTED_SNP_POS []int

+ func (I *Index) Init(genome_file, snp_file, index_file, rev_index_file string, read_len int, ...)

+ func (I Index) BackwardDistanceMulti(s, t []byte, pos int) (int, int, int, int, map[int][]byte, [][][]byte, bool)

+ func (I Index) BackwardSearchFrom(index fmi.Index, pattern []byte, start_pos int) []int

+ func (I Index) BackwardTraceBack(s, t []byte, m, n int, S map[int][]byte, T [][][]byte, pos int) map[int][]byte

+ func (I Index) FindExtensions(read []byte, s_pos, e_pos int, match_pos int) (int, []byte, []byte, []byte, []byte, map[int][]byte, map[int][]byte, bool)

+ func (I Index) FindSeeds(read []byte, p int) (int, int, []int, bool)

+ func (I Index) ForwardDistanceMulti(s, t []byte, pos int) (int, int, int, int, map[int][]byte, [][][]byte, bool)

+ func (I Index) ForwardTraceBack(s, t []byte, m, n int, S map[int][]byte, T [][][]byte, pos int) map[int][]byte

+ type SNP struct

+ type SNPProf struct

+ SNP_Call map[int][]byte

+ SNP_Prob map[int][]int

+ SNP_Prof map[int][][]byte

+ func (S *SNPProf) Init(genome_file, snp_file, index_file, rev_index_file string, read_len int, ...)

+ func (S *SNPProf) UpdateSNPProfile(read1, read2 []byte) bool

+ func (S SNPProf) CallSNP()

+ func (S SNPProf) FindSNPProfile(read1, read2 []byte) (map[int][][]byte, bool)

+ func (S SNPProf) SNPCall_tofile(file_name string)

May 5, 2014

Changes in this version

+ var DIST_THRES int

+ var ITER_NUM int

+ var MAXIMUM_MATCH int

+ func IntervalHasSNP(A []int, i, j int) bool

+ type Aligner struct

+ SAME_LEN_SNP map[int]int

+ SEQ []byte

+ SNP_PROFILE map[int][][]byte

+ SORTED_SNP_POS []int

+ func (A *Aligner) FindSNPProfile_read(read []byte) (map[int][][]byte, bool)

+ func (A *Aligner) Init(genome_file, snp_file, index_file, rev_index_file string, read_len int, ...)

+ func (A Aligner) FindExtension(read []byte, s_pos, e_pos int, match_pos int) (int, []byte, []byte, []byte, []byte, map[int][]byte, map[int][]byte, bool)

+ type SNPCaller struct

+ SNP_Call map[int][]byte

+ SNP_Prob map[int][]int

+ SNP_Prof map[int][][]byte

+ func (S *SNPCaller) Init(genome_file, snp_file, index_file, rev_index_file string, read_len int, ...)

+ func (S *SNPCaller) UpdateSNPProfile(read []byte) bool

+ func (S SNPCaller) CallSNP() (map[int][]byte, map[int][]int)

+ func (S SNPCaller) SNPCall_tofile(file_name string)

+ type Search struct

+ FMI fmi.Index

+ REV_FMI fmi.Index

+ func (S *Search) Init(index_file, rev_index_file string, n int)

+ func (S Search) BackwardSearch(index fmi.Index, pattern []byte, start_pos int) []int

+ func (S Search) FindLCS(read []byte, p int) (int, int, []int, bool)