track.nim

import hts/files
import strutils
import tables
import json
import strformat
import hts/bam
import os

type Track* = object
  file_type*: FileType
  path*:string
  name*: string
  n_tracks*:int
  reference*:string
  # if region is specified, then we base64 encode the track, otherwise we
  # use the server.
  region*:string

proc isremote*(path:string): bool =
  result = path.startswith("http") or path.startswith("ftp:")

proc get_type*(T:Track): string =
  if T.path.endsWith(".cram") or T.path.endsWith(".bam"):
    return "alignment"
  case T.file_type
  of FileType.CRAM, FileType.BAM:
    return "alignment"
  of FileType.VCF, FileType.BCF:
    return "variant"
  of FileType.BED:
    return "annotation"
  else:
    if T.path.endsWith(".bed") or T.path.endsWith(".bed.gz") or T.path.endsWith(".bedgraph"):
      return "annotation"
    if T.path.endsWith(".bw") or T.path.endsWith(".wig") or T.path.toLowerAscii.endswith(".bigwig"):
      return "wig"
    for ext in ["gff", "gff3", "gff3.gz", "gff.gz", "gtf", "gtf.gz"]:
      if T.path.endsWith("." & ext):
        return "annotation"

    raise newException(ValueError, "unknown file type for " & $T.file_type)

proc height*(T:Track): int =
  var mult = 1
  if T.n_tracks < 3:
    mult = 2
  if T.path.endsWith(".cram") or T.path.endsWith(".bam"):
    return 250 * mult
  case T.file_type
  of FileType.CRAM, FileType.BAM:
    return 250 * mult
  of FileType.VCF, FileType.BCF:
    return 60
  else:
    return 50

proc format*(T:Track): string =
  if T.path.split('#')[0].endsWith(".cram"):
    if T.region != "": return "bam"
    return "cram"
  if T.path.split('#')[0].endsWith(".bam"):
    return "bam"
  if T.path.split('#')[0].endsWith(".bed") or T.path.split('#')[0].endsWith(".bed.gz") or T.path.split('#')[0].endsWith(".bedgraph"):
    return "bed"
  if T.path.split('#')[0].endsWith(".bw") or T.path.split('#')[0].endsWith(".wig") or T.path.split('#')[0].toLowerAscii.endswith(".bigwig"):
    return "wig"

  for ext in ["gtf", "gtf.gz"]:
    if T.path.endsWith("." & ext):
      return "gtf"

  for ext in ["gff", "gff.gz", "gff3", "gff3.gz"]:
    if T.path.endsWith("." & ext):
      return "gff"

  case T.file_type
  of FileType.CRAM, FileType.BAM:
    return ($T.file_type).toLowerAscii
  of FileType.VCF, FileType.BCF:
    return "vcf"
  of FileType.BED:
    return "annotation"
  else:
    raise newException(ValueError, "unknown format for " & $T.file_type)

template isdata(path:string): bool =
  path.startswith("data:")

proc url(t:Track): string =
  if t.path.isremote or t.path.isdata:
    return t.path
  result = &"/data/tracks/{extractFileName(t.path)}"

proc index_ext*(t:Track): string =
  if t.path.isremote:
    case splitFile(t.path).ext
    of ".bam": return ".bai"
    of ".cram": return ".crai"
    of ".vcf.gz", "bed.gz": return ".tbi"

  case t.file_type
  of FileType.CRAM:
    result = ".crai"
  of FileType.BAM:
    result = ".bai"
  of FileType.VCF:
    result = ".tbi"
  else:
    if t.path.endsWith(".bed.gz"):
      return ".tbi"
    raise newException(ValueError, "unsupported file type:" & $t.file_type)

proc indexUrl*(t:Track): string =
  result = t.url & t.index_ext

proc `%`*(T:Track): JsonNode =
  var fields = initOrderedTable[string, JsonNode](4)
  fields["type"] = % T.get_type
  if T.format != "wig":
    fields["format"] = % T.format
  fields["url"] = % T.url
  if T.region == "":
    try:
      fields["indexURL"] = % T.indexUrl
    except ValueError:
      discard

  if fields["type"] == % "annotation":
    fields["displayMode"] = % "SQUISHED"
  fields["name"] = % T.name
  if T.height != 0:
    fields["height"] = % T.height
  if T.file_type in  {FileType.CRAM, FileType.BAM}:
    fields["alignmentRowHeight"] = % 8
    fields["colorBy"] = % "strand"
    fields["coverageTrackHeight"] = % 24
    fields["showSoftClips"] = % true
    fields["viewAsPairs"] = % true
  return JsonNode(kind: JObject, fields: fields)

proc `$`*(T:Track): string =
  return $(%T)