module

Paftools

paftools.cr — Crystal port of paftools.js (minimap2 companion utilities)

Constants

VERSION = "2.30 (Crystal port)"

Class methods

cmd_asmgene(args : Array(String)) : Int32

cmd_asmstat(args : Array(String)) : Int32

cmd_bedcov(args : Array(String)) : Int32

cmd_call(args : Array(String)) : Int32

cmd_delta2paf(args : Array(String)) : Int32

cmd_gff2bed(args : Array(String)) : Int32

cmd_gff2junc(args : Array(String)) : Int32

cmd_liftover(args : Array(String)) : Int32

cmd_longcs2seq(args : Array(String)) : Int32

cmd_sam2paf(args : Array(String)) : Int32

cmd_splice2bed(args : Array(String)) : Int32

cmd_stat(args : Array(String)) : Int32

cmd_vcfpair(args : Array(String)) : Int32

cmd_view(args : Array(String)) : Int32

cov_len(regs : Array(Tuple(Int32, Int32))) : Int64

intv_build(a : Array(Tuple(Int32, Int32))) : Array(Int32)

intv_merge(a : Array(Tuple(Int32, Int32)))

intv_ovlp(a : Array(Tuple(Int32, Int32)), idx : Array(Int32), st : Int32, en : Int32) : Array(Tuple(Int32, Int32))

intv_ovlp_idx(a : Array(Tuple(Int32, Int32)), idx : Array(Int32), st : Int32, en : Int32) : Array(Int32)

Returns indices into a of all intervals overlapping [st, en)

intv_sort(a : Array(Tuple(Int32, Int32)))

open_in(fn : String, &)

read_fasta(fn : String) : Tuple(Hash(String, String), Array(Tuple(String, Int32)))

run(argv : Array(String)) : Int32