module HTS::LibHTS
Constants
- BAM_CBACK
- BAM_CDEL
- BAM_CDIFF
- BAM_CEQUAL
- BAM_CHARD_CLIP
- BAM_CIGAR_MASK
- BAM_CIGAR_SHIFT
- BAM_CIGAR_STR
- BAM_CIGAR_STR_PADDED
- BAM_CIGAR_TYPE
- BAM_CINS
- BAM_CMATCH
constants
- BAM_CPAD
- BAM_CREF_SKIP
- BAM_CSOFT_CLIP
- BAM_FDUP
- BAM_FMREVERSE
- BAM_FMUNMAP
- BAM_FPAIRED
- BAM_FPROPER_PAIR
- BAM_FQCFAIL
- BAM_FREAD1
- BAM_FREAD2
- BAM_FREVERSE
- BAM_FSECONDARY
- BAM_FSUPPLEMENTARY
- BAM_FUNMAP
- BCF1_DIRTY_ALS
- BCF1_DIRTY_FLT
- BCF1_DIRTY_ID
- BCF1_DIRTY_INF
- BCF_BT_CHAR
- BCF_BT_FLOAT
- BCF_BT_INT16
- BCF_BT_INT32
- BCF_BT_INT64
- BCF_BT_INT8
- BCF_BT_NULL
- BCF_DT_CTG
- BCF_DT_ID
- BCF_DT_SAMPLE
- BCF_ERR_CHAR
- BCF_ERR_CTG_INVALID
- BCF_ERR_CTG_UNDEF
- BCF_ERR_LIMITS
- BCF_ERR_NCOLS
- BCF_ERR_TAG_INVALID
- BCF_ERR_TAG_UNDEF
- BCF_HL_CTG
- BCF_HL_FLT
constants
- BCF_HL_FMT
- BCF_HL_GEN
- BCF_HL_INFO
- BCF_HL_STR
- BCF_HT_FLAG
- BCF_HT_INT
- BCF_HT_LONG
- BCF_HT_REAL
- BCF_HT_STR
- BCF_UN_ALL
- BCF_UN_FLT
- BCF_UN_FMT
- BCF_UN_IND
- BCF_UN_INFO
- BCF_UN_SHR
- BCF_UN_STR
constants
- BCF_VL_A
- BCF_VL_FIXED
- BCF_VL_G
- BCF_VL_R
- BCF_VL_VAR
- BamHdr
- FaiFormatOptions
faidx
- HtsCompression
- HtsExactFormat
- HtsFmtOption
- HtsFormatCategory
- HtsLogLevel
hts
- SamFile
- VCF_BND
- VCF_INDEL
- VCF_MNP
- VCF_OTHER
- VCF_OVERLAP
- VCF_REF
- VCF_SNP
Public Class Methods
attach_function(*)
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Calls superclass method
# File lib/hts/libhts.rb, line 13 def self.attach_function(*) super rescue FFI::NotFoundError => e warn e.message end
bam_cigar_gen(l, o)
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# File lib/hts/libhts/sam.rb, line 37 def bam_cigar_gen(l, o) l << BAM_CIGAR_SHIFT | o end
bam_cigar_op(c)
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# File lib/hts/libhts/sam.rb, line 25 def bam_cigar_op(c) c & BAM_CIGAR_MASK end
bam_cigar_opchr(c)
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# File lib/hts/libhts/sam.rb, line 33 def bam_cigar_opchr(c) ("#{BAM_CIGAR_STR}??????")[bam_cigar_op(c)] end
bam_cigar_oplen(c)
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# File lib/hts/libhts/sam.rb, line 29 def bam_cigar_oplen(c) c >> BAM_CIGAR_SHIFT end
bam_cigar_type(o)
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# File lib/hts/libhts/sam.rb, line 41 def bam_cigar_type(o) BAM_CIGAR_TYPE >> (o << 1) & 3 end
bam_get_aux(b)
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# File lib/hts/libhts/sam.rb, line 86 def bam_get_aux(b) b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1) + b[:core][:l_qseq] end
bam_get_cigar(b)
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# File lib/hts/libhts/sam.rb, line 74 def bam_get_cigar(b) b[:data] + b[:core][:l_qname] end
bam_get_l_aux(b)
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# File lib/hts/libhts/sam.rb, line 90 def bam_get_l_aux(b) b[:l_data] - (b[:core][:n_cigar] << 2) - b[:core][:l_qname] - b[:core][:l_qseq] - ((b[:core][:l_qseq] + 1) >> 1) end
bam_get_qname(b)
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# File lib/hts/libhts/sam.rb, line 70 def bam_get_qname(b) b[:data] end
bam_get_qual(b)
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# File lib/hts/libhts/sam.rb, line 82 def bam_get_qual(b) b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] + ((b[:core][:l_qseq] + 1) >> 1) end
bam_get_seq(b)
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# File lib/hts/libhts/sam.rb, line 78 def bam_get_seq(b) b[:data] + (b[:core][:n_cigar] << 2) + b[:core][:l_qname] end
bam_is_mrev(b)
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# File lib/hts/libhts/sam.rb, line 66 def bam_is_mrev(b) b[:core][:flag] & BAM_FMREVERSE != 0 end
bam_is_rev(b)
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# File lib/hts/libhts/sam.rb, line 62 def bam_is_rev(b) b[:core][:flag] & BAM_FREVERSE != 0 end
bam_seqi(s, i)
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# File lib/hts/libhts/sam.rb, line 94 def bam_seqi(s, i) s[(i) >> 1].read_uint8 >> ((~i & 1) << 2) & 0xf end
bcf_hdr_nsamples(hdr)
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# File lib/hts/libhts/vcf.rb, line 60 def bcf_hdr_nsamples(hdr) hdr[:n][BCF_DT_SAMPLE] end
sam_itr_next(htsfp, itr, r)
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Get the next read from a SAM/BAM/CRAM iterator
# File lib/hts/libhts/sam.rb, line 442 def self.sam_itr_next(htsfp, itr, r) # FIXME: check if htsfp is compressed BGZF hts_log_error("Null iterator") if itr.null? # FIXME: check multi hts_itr_next(htsfp[:fp][:bgzf], itr, r, htsfp) end