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Fix most warnings
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The "{.gcsafe.}" change might not be needed. The real fix for that
was bluenote10/nim-heap#7
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Christopher Dunn committed May 24, 2019
1 parent 3555d3f commit 7b70394
Showing 1 changed file with 89 additions and 88 deletions.
177 changes: 89 additions & 88 deletions src/falcon/rr_hctg_track.nim
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ from hashes import nil
from json import nil
import json
from os import nil
from ospaths import nil
from osproc import nil
#from "pure/osproc.nim" import nil
from parsecsv import nil
Expand All @@ -34,12 +33,12 @@ type
mytable = tables.Table[string, seq[mytuple]]
myprioritytable = tables.Table[string, binaryheap.Heap[mytuple]]

proc toseq(src: str9): seq[int] =
var dst = newSeq[int](9)
assert len(dst) == 9
for i in 0..<9:
dst[i] = src[i].int
return dst
#proc toseq(src: str9): seq[int] =
# var dst = newSeq[int](9)
# assert len(dst) == 9
# for i in 0..<9:
# dst[i] = src[i].int
# return dst
proc fromstring(src: string): str9 =
# dst must be same length as src
assert len(src) == 9
Expand All @@ -58,8 +57,8 @@ proc tostring(src: str9, dst: var string) =
for i in 0..<9:
dst[i] = src[i]

proc hash(x: str9): hashes.Hash =
return hashes.hash(tostring(x))
#proc hash(x: str9): hashes.Hash =
# return hashes.hash(tostring(x))

proc unpack_type*(ss: msgpack4nim.MsgStream, x: var str9) =
var str: string
Expand All @@ -73,10 +72,10 @@ proc pack_type*(ss: msgpack4nim.MsgStream, x: str9) =
proc pack_type*(ss: msgpack4nim.MsgStream, x: binaryheap.Heap[mytuple]) =
let xseq: seq[mytuple] = sequtils.toSeq(binaryheap.items(x)) # unsorted
msgpack4nim.pack(ss, xseq)
proc `$`(x: str9): string =
return tostring(x)
proc `$`(x: mytuple): string =
return "[$#, $#]" % [$x.score, $x.rid]
#proc `$`(x: str9): string =
# return tostring(x)
#proc `$`(x: mytuple): string =
# return "[$#, $#]" % [$x.score, $x.rid]
#[
proc `$`(x: Table): string =
var ss = streams.newStringStream()
Expand All @@ -98,25 +97,25 @@ proc `$`(x: Table): string =
ss.setPosition(0)
return ss.readAll()
]#
proc `$`(x: binaryheap.Heap[mytuple]): string =
var ss = streams.newStringStream()
ss.write("len=" & $binaryheap.size(x))
ss.write("[")
var first = true
for v in binaryheap.items(x):
if first:
first = false
else:
ss.write(", ")
ss.write("'")
ss.write($v)
ss.write("'")
ss.write("]")
ss.setPosition(0)
return ss.readAll()


proc mytuple_cmp(x, y: mytuple): int =
#proc `$`(x: binaryheap.Heap[mytuple]): string =
# var ss = streams.newStringStream()
# ss.write("len=" & $binaryheap.size(x))
# ss.write("[")
# var first = true
# for v in binaryheap.items(x):
# if first:
# first = false
# else:
# ss.write(", ")
# ss.write("'")
# ss.write($v)
# ss.write("'")
# ss.write("]")
# ss.setPosition(0)
# return ss.readAll()


proc mytuple_cmp(x, y: mytuple): int = #{.gcsafe.} =
if x.score < y.score: return -1
if x.score > y.score: return 1
for i in 0..<9:
Expand All @@ -135,11 +134,11 @@ proc get_fns_from_json*(json_fn: string): seq[string] =
log("Reading JSON from '", json_fn, "'")
let jcontent = system.readFile(json_fn)
result = to(json.parseJson(jcontent), seq[string]) # json.to()
let fofn_dir = ospaths.parentDir(json_fn) # "" is ok
let fofn_dir = os.parentDir(json_fn) # "" is ok
for i in 0 ..< result.len:
let fn = result[i]
if not ospaths.isAbsolute(fn):
result[i] = ospaths.joinPath(fofn_dir, fn)
if not os.isAbsolute(fn):
result[i] = os.joinPath(fofn_dir, fn)

proc fillTuple[T: tuple, V](input: openarray[V]): T =
#assert input.len == len(result.fields)
Expand All @@ -164,7 +163,7 @@ proc stream_get_rid_to_ctg_slow(infile: streams.Stream): auto =
# rid_to_ctg[t.rid] = newSeq[string]()
#rid_to_ctg[t.rid].add(t.ctg)
if not rid_to_ctg.contains(t.rid):
rid_to_ctg[t.rid] = sets.initSet[string](2)
rid_to_ctg[t.rid] = sets.initHashSet[string](2)
rid_to_ctg[t.rid].incl(t.ctg)
return rid_to_ctg

Expand All @@ -187,7 +186,7 @@ proc stream_get_rid_to_ctg(ss: streams.Stream, fn="rid_to_ctg"): auto =
let ctg = csv.row[3]
#log("rid=", rid, ", ctg=", ctg)
if not rid_to_ctg.contains(rid):
rid_to_ctg[rid] = sets.initSet[string](2)
rid_to_ctg[rid] = sets.initHashSet[string](2)

var global_logged_rid_to_ctg {.global.} = false
if (not global_logged_rid_to_ctg) and (ctg in rid_to_ctg[rid]):
Expand All @@ -197,14 +196,14 @@ proc stream_get_rid_to_ctg(ss: streams.Stream, fn="rid_to_ctg"): auto =
rid_to_ctg[rid].incl(ctg)
return rid_to_ctg

proc get_rid_to_ctg_slow(fn: string): auto =
log("In get_rid_to_ctg_slow(): len=", sys.filelength(fn), " for file '", fn, "'")
let
ss = streams.newFileStream(fn)
assert(not ss.isNil())
defer:
streams.close(ss)
return stream_get_rid_to_ctg_slow(ss)
#proc get_rid_to_ctg_slow(fn: string): auto =
# log("In get_rid_to_ctg_slow(): len=", sys.filelength(fn), " for file '", fn, "'")
# let
# ss = streams.newFileStream(fn)
# assert(not ss.isNil())
# defer:
# streams.close(ss)
# return stream_get_rid_to_ctg_slow(ss)

proc get_rid_to_ctg*(fn: string): auto =
#let content = readFile(fn)
Expand All @@ -225,7 +224,7 @@ proc get_rid_to_ctg*(fn: string): auto =

#min_len, bestn, rid_to_ctg, rid_to_phase
type
Settings* = object {.requiresInit.}
Settings* {.requiresInit.} = object
n_core*: int #48
file_list*: seq[string]
db_fn*: string #"?/raw_reads.db"
Expand Down Expand Up @@ -263,25 +262,25 @@ proc stream_get_oid_to_phase(ss: streams.Stream, fn: string): auto =
oid_to_phase[oid] = p
return oid_to_phase

proc stream_get_oid_to_phase_slow(ss: streams.Stream, fn: string): auto =
let oid_to_phase = tables.newTable[string, Phase]()
log("In stream_get_oid_to_phase_slow()")

var line: TaintedString = ""
while streams.readLine(ss, line):
let row = line.splitWhitespace()
if len(row) == 0: continue
#let t: TRow = fillTuple[TRow, string](row)

#log("phased_reads_row:", $row)
let p: Phase = (
ctg_id: row[1],
blockn: strutils.parseInt(row[2]).int16,
phase: strutils.parseInt(row[3]).int16
)
let oid = row[6]
oid_to_phase[oid] = p
return oid_to_phase
#proc stream_get_oid_to_phase_slow(ss: streams.Stream, fn: string): auto =
# let oid_to_phase = tables.newTable[string, Phase]()
# log("In stream_get_oid_to_phase_slow()")
#
# var line: TaintedString = ""
# while streams.readLine(ss, line):
# let row = line.splitWhitespace()
# if len(row) == 0: continue
# #let t: TRow = fillTuple[TRow, string](row)
#
# #log("phased_reads_row:", $row)
# let p: Phase = (
# ctg_id: row[1],
# blockn: strutils.parseInt(row[2]).int16,
# phase: strutils.parseInt(row[3]).int16
# )
# let oid = row[6]
# oid_to_phase[oid] = p
# return oid_to_phase

proc stream_get_rid_to_phase(rawread_ids_fn: string,
oid_to_phase: TableRef[string, Phase]): auto =
Expand Down Expand Up @@ -337,7 +336,7 @@ var global_rid_to_phase {.threadvar.}: ref seq[Phase]
proc tr_stage1(la4falcon_stream: streams.Stream, fn: string, min_len, bestn: int): myprioritytable =
# for each read in the b-read column inside the LAS files, we
#keep top `bestn` hits with a priority queue through all overlaps
result = tables.initTable[string, binaryheap.Heap[mytuple]](1024)
var myresult = tables.initTable[string, binaryheap.Heap[mytuple]](1024)

var
csv: parsecsv.CsvParser
Expand All @@ -350,9 +349,10 @@ proc tr_stage1(la4falcon_stream: streams.Stream, fn: string, min_len, bestn: int
q_id = csv.row[0]
t_id = csv.row[1]
overlap_len = -strutils.parseInt(csv.row[2])
idt = strutils.parseFloat(csv.row[3])
(q_s, q_e, q_l) = (strutils.parseInt(csv.row[5]), strutils.parseInt(csv.row[6]), strutils.parseInt(csv.row[7]))
(t_s, t_e, t_l) = (strutils.parseInt(csv.row[9]), strutils.parseInt(csv.row[10]), strutils.parseInt(csv.row[11]))
#idt = strutils.parseFloat(csv.row[3])
#(q_s, q_e, q_l) = (strutils.parseInt(csv.row[5]), strutils.parseInt(csv.row[6]), strutils.parseInt(csv.row[7]))
#(t_s, t_e, t_l) = (strutils.parseInt(csv.row[9]), strutils.parseInt(csv.row[10]), strutils.parseInt(csv.row[11]))
t_l = strutils.parseInt(csv.row[11])
if t_l < min_len:
continue
if q_id notin global_rid_to_ctg:
Expand All @@ -373,23 +373,24 @@ proc tr_stage1(la4falcon_stream: streams.Stream, fn: string, min_len, bestn: int
if (q_phase.ctg_id == t_phase.ctg_id and q_phase.blockn == t_phase.blockn and
q_phase.phase != t_phase.phase):
continue
if t_id notin result:
result[t_id] = binaryheap.newHeap[mytuple](mytuple_cmp)
if t_id notin myresult:
myresult[t_id] = binaryheap.newHeap[mytuple](mytuple_cmp)
let it: mytuple = (score: overlap_len, rid: fromstring(q_id))
#log(" rid:", $fromstring(q_id))
#log(" it:", $it)
if binaryheap.size(result[t_id]) < bestn:
binaryheap.push(result[t_id], it)
#log(" heap:", $result[t_id])
if binaryheap.size(myresult[t_id]) < bestn:
binaryheap.push(myresult[t_id], it)
#log(" heap:", $myresult[t_id])
else:
discard binaryheap.pushPop(result[t_id], it)
#log(" heap now:", $result[t_id])
discard binaryheap.pushPop(myresult[t_id], it)
#log(" heap now:", $myresult[t_id])
return myresult

proc captureCmd(cmd: string): auto =
#log("$$($#)" % [cmd])
let options: set[osproc.ProcessOption] = {osproc.poUsePath, osproc.poEvalCommand, osproc.poEchoCmd}
result = osproc.execProcess(cmd, options=options)
log(" len(stdout)==", len(result))
#proc captureCmd(cmd: string): auto =
# #log("$$($#)" % [cmd])
# let options: set[osproc.ProcessOption] = {osproc.poUsePath, osproc.poEvalCommand, osproc.poEchoCmd}
# result = osproc.execProcess(cmd, options=options)
# log(" len(stdout)==", len(result))

proc run_tr_stage1(db_fn, fn: string, min_len, bestn: int): string =
let cmd = "LA4Falcon -m $# $#" % [db_fn, fn]
Expand Down Expand Up @@ -530,8 +531,8 @@ proc run_stage2*(
out_f.close()

type ScoreCount = tuple[score: int, count: int]
proc `$`(val: ScoreCount): auto =
return "(" & $val[0] & ", " & $val[1] & ")"
#proc `$`(val: ScoreCount): auto =
# return "(" & $val[0] & ", " & $val[1] & ")"

log(" Writing ctg/scores for ", len(bread_to_areads), " breads.")
var rid = newString(9) # same length as str9
Expand Down Expand Up @@ -603,12 +604,12 @@ proc test() =
assert $res["000000026"] == "@[000000F, 000000C]", $res["000000026"]
assert $res["000000287"] == "@[000000F_02]", $res["000000287"]
echo "Success."
block:
let fn = "/lustre/hpcprod/cdunn/jira/se-809/run/4-quiver/read_maps/read_to_contig_map"
#let res = get_rid_to_ctg(fn)
#block:
# let fn = "/lustre/hpcprod/cdunn/jira/se-809/run/4-quiver/read_maps/read_to_contig_map"
# let res = get_rid_to_ctg(fn)

proc main() =
test()
#proc main() =
# test()

if isMainModule:
test()

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