module HTS::LibHTS2

Extended Modules

• HTS::LibHTS2

Defined in:

hts/libhts.cr
hts/libhts2/bgzf.cr
hts/libhts2/hfile.cr
hts/libhts2/sam.cr
hts/libhts2/vcf.cr

Constant Summary

BAM_CBACK = 9

BAM_CDEL = 2

BAM_CDIFF = 8

BAM_CEQUAL = 7

BAM_CHARD_CLIP = 5

BAM_CIGAR_MASK = 15

BAM_CIGAR_SHIFT = 4

BAM_CIGAR_STR = "MIDNSHP=XB"

BAM_CIGAR_TYPE = 246183

BAM_CINS = 1

BAM_CMATCH = 0

constants

BAM_CPAD = 6

BAM_CREF_SKIP = 3

BAM_CSOFT_CLIP = 4

BAM_FDUP = 1024

BAM_FMREVERSE = 32

BAM_FMUNMAP = 8

BAM_FPAIRED = 1

BAM_FPROPER_PAIR = 2

BAM_FQCFAIL = 512

BAM_FREAD1 = 64

BAM_FREAD2 = 128

BAM_FREVERSE = 16

BAM_FSECONDARY = 256

BAM_FSUPPLEMENTARY = 2048

BAM_FUNMAP = 4

BCF1_DIRTY_ALS = 2

BCF1_DIRTY_FLT = 4

BCF1_DIRTY_ID = 1

BCF1_DIRTY_INF = 8

BCF_BT_CHAR = 7

BCF_BT_FLOAT = 5

BCF_BT_INT16 = 2

BCF_BT_INT32 = 3

BCF_BT_INT64 = 4

BCF_BT_INT8 = 1

BCF_BT_NULL = 0

BCF_DT_CTG = 1

BCF_DT_ID = 0

BCF_DT_SAMPLE = 2

BCF_ERR_CHAR = 16

BCF_ERR_CTG_INVALID = 32

BCF_ERR_CTG_UNDEF = 1

BCF_ERR_LIMITS = 8

BCF_ERR_NCOLS = 4

BCF_ERR_TAG_INVALID = 64

BCF_ERR_TAG_UNDEF = 2

BCF_HL_CTG = 3

BCF_HL_FLT = 0

constants

BCF_HL_FMT = 2

BCF_HL_GEN = 5

BCF_HL_INFO = 1

BCF_HL_STR = 4

BCF_HT_FLAG = 0

BCF_HT_INT = 1

BCF_HT_LONG = (BCF_HT_INT | 256)

BCF_HT_REAL = 2

BCF_HT_STR = 3

BCF_UN_ALL = (BCF_UN_SHR | BCF_UN_FMT)

BCF_UN_FLT = 2

BCF_UN_FMT = 8

BCF_UN_IND = BCF_UN_FMT

BCF_UN_INFO = 4

BCF_UN_SHR = ((BCF_UN_STR | BCF_UN_FLT) | BCF_UN_INFO)

BCF_UN_STR = 1

BCF_VL_A = 2

BCF_VL_FIXED = 0

BCF_VL_G = 3

BCF_VL_R = 4

BCF_VL_VAR = 1

VCF_BND = 16

VCF_INDEL = 4

VCF_MNP = 2

VCF_OTHER = 8

VCF_OVERLAP = 32

VCF_REF = 0

VCF_SNP = 1

Macro Summary

• alias_method(new_name, old_name)

Instance Method Summary

• #bam_cigar_gen(l, o)
• #bam_cigar_op(c)

  macros

• #bam_cigar_opchr(c)
• #bam_cigar_oplen(c)
• #bam_cigar_type(o)
• #bam_get_aux(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_get_cigar(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_get_l_aux(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_get_qname(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_get_qual(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_get_seq(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_is_mrev(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_is_rev(b : Pointer(HTS::LibHTS::Bam1T))
• #bam_seqi(s, i)
• #bcf_alleles2gt(a, b)
• #bcf_clear1(*args)
• #bcf_close(*args)

  alias_method bcf_flush hts_flush

• #bcf_destroy1(*args)
• #bcf_empty1(*args)
• #bcf_get_format_char(hdr, line, tag, dst, ndst)
• #bcf_get_format_float(hdr, line, tag, dst, ndst)
• #bcf_get_format_int32(hdr, line, tag, dst, ndst)
• #bcf_get_genotypes(hdr, line, dst, ndst)
• #bcf_get_info_flag(hdr, line, tag, dst, ndst)
• #bcf_get_info_float(hdr, line, tag, dst, ndst)
• #bcf_get_info_int32(hdr, line, tag, dst, ndst)
• #bcf_get_info_string(hdr, line, tag, dst, ndst)
• #bcf_gt_allele(val)
• #bcf_gt_is_missing(val)
• #bcf_gt_is_phased(idx)
• #bcf_gt_missing
• #bcf_gt_phased(idx)
• #bcf_gt_unphased(idx)
• #bcf_hdr_id2name(hdr, rid)
• #bcf_hdr_int2id(hdr, type, int_id)
• #bcf_hdr_name2id(hdr, id)
• #bcf_hdr_nsamples(hdr : Pointer(HTS::LibHTS::BcfHdrT))
• #bcf_init1(*args)
• #bcf_open(*args)
• #bcf_read1(*args)
• #bcf_update_format_char(hdr, line, key, values, n)
• #bcf_update_format_float(hdr, line, key, values, n)
• #bcf_update_format_int32(hdr, line, key, values, n)
• #bcf_update_genotypes(hdr, line, gts, n)
• #bcf_update_info_flag(hdr, line, key, string, n)
• #bcf_update_info_float(hdr, line, key, values, n)
• #bcf_update_info_int32(hdr, line, key, values, n)
• #bcf_update_info_string(hdr, line, key, string)
• #bcf_write1(*args)
• #bgzf_tell(fp)
• #htell(fp)
• #sam_itr_next(htsfp, itr, r)
• #vcf_close(*args)
• #vcf_format1(*args)
• #vcf_open(*args)
• #vcf_parse1(*args)
• #vcf_read1(*args)
• #vcf_write1(*args)

Macro Detail

Instance Method Detail