From 2f51cacc4bb33658bbb6423df370e651d571d125 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Sat, 16 Jan 2021 17:48:28 +1100
Subject: [PATCH] distr deps
---
README.md | 16 +++++++++++++++-
src/sscocaller.nim | 24 ++++++++++++------------
sscocaller.nimble | 4 ++--
3 files changed, 29 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index 8eef208..5e84fe2 100644
--- a/README.md
+++ b/README.md
@@ -43,6 +43,7 @@ Examples
## Setup/installation
+### Install with nimble
`sscocaller` uses `hts-nim`(https://github.com/brentp/hts-nim) that requires the `hts-lib` library. If you are building the `sscocaller` from
source, you would need to install `hts-lib`
@@ -58,12 +59,25 @@ ls -lh $HOME/htslib/*.so
Then, `sscocaller` can be installed using `nimble`
-### Install with nimble
+
`nimble install https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git`
The built binary in $HOME/.nimble/bin/sscocaller
+### Using docker
+
+`sscocaller` is also available in docker image [`svirlyu/sscocaller`] https://hub.docker.com/r/svirlyu/sscocaller
+
+```
+docker run -it svirlyu/sscocaller
+
+## execute sscocaller
+/usr/bin/sscocaller -h
+
+```
+
+
### Static builds
The static bianry can be simply downloaded which works for GNU/Linux type OS:
\ No newline at end of file
diff --git a/src/sscocaller.nim b/src/sscocaller.nim
index 88756df..196f360 100755
--- a/src/sscocaller.nim
+++ b/src/sscocaller.nim
@@ -13,7 +13,7 @@ import hts
import tables
import sequtils
import math
-from rmath import dbinom
+import distributions/rmath
import streams
#echo paramCount(), " ", paramStr(1)
@@ -201,7 +201,7 @@ proc sscocaller(argv: var seq[string]): int =
proc getTrans(pos1:int64,pos2:int64,cmPmb=0.1): float =
if pos2<pos1:
quit "Wrong order of snps"
- var rec = 1-exp(-float(pos2-pos1)*1e-8*cmPmb) # for autosomes 1*cmPbm cM per Mb
+ var rec = 1-math.exp(-float(pos2-pos1)*1e-8*cmPmb) # for autosomes 1*cmPbm cM per Mb
return rec
#maxTotalReads:int
proc countAllele(rec:Variant, ibam:Bam, chrom:string, mapq: int,
@@ -327,8 +327,8 @@ proc sscocaller(argv: var seq[string]): int =
if scSpermSeq[ithSperm].viNodeseq.len==0:
echo "first node to ", ithSperm
var currentViNode = ViNode()
- currentViNode.pathScore[stateRef] = ln(initProb[stateRef])+emissionArray[stateRef]
- currentViNode.pathScore[stateAlt] = ln(initProb[stateAlt])+emissionArray[stateAlt]
+ currentViNode.pathScore[stateRef] = math.ln(initProb[stateRef])+emissionArray[stateRef]
+ currentViNode.pathScore[stateAlt] = math.ln(initProb[stateAlt])+emissionArray[stateAlt]
currentViNode.pathState[stateRef] = stateN
currentViNode.pathState[stateAlt] = stateN
currentViNode.state = stateN
@@ -342,8 +342,8 @@ proc sscocaller(argv: var seq[string]): int =
else:
#echo "additional node to a cell"
let preVNode = scSpermSeq[ithSperm].viNodeseq[high(scSpermSeq[ithSperm].viNodeseq)]
- var ltransProb = ln(getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
- var lnoTransProb = ln(1-getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
+ var ltransProb = math.ln(getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
+ var lnoTransProb = math.ln(1-getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
var currentViNode = ViNode()
# ref/alt -> ref
var refTref = preVNode.pathScore[stateRef] + lnoTransProb
@@ -431,7 +431,7 @@ proc sscocaller(argv: var seq[string]): int =
else: # there is transition to different state: ref(start) to alt(end) now output the segment info
posStart = scSpermSeq[ithSperm].viNodeseq[^(i)].pos
#leftGapSize = scSpermSeq[ithSperm].viNodeseq[^(i)].pos - scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos
- leftGap=[ln(transProb),ln(1-transProb)]
+ leftGap=[math.ln(transProb),math.ln(1-transProb)]
inferProb+=leftGap[0]
reverseProb+=leftGap[1]
viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2")
@@ -454,7 +454,7 @@ proc sscocaller(argv: var seq[string]): int =
else:
## state transit
posStart = scSpermSeq[ithSperm].viNodeseq[^(i)].pos
- leftGap=[ln(transProb),ln(1-transProb)]
+ leftGap=[math.ln(transProb),math.ln(1-transProb)]
inferProb += leftGap[0]
reverseProb += leftGap[1]
viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
@@ -485,12 +485,12 @@ proc sscocaller(argv: var seq[string]): int =
scSpermSeq[ithSperm].viNodeseq[1].pos,
cmPmb=cmPmb)
if scSpermSeq[ithSperm].viNodeseq[0].state == stateRef:
- inferProb = currentEm[stateRef]+ln(transProb)
- reverseProb = currentEm[stateAlt]+ln(1-transProb)
+ inferProb = currentEm[stateRef]+math.ln(transProb)
+ reverseProb = currentEm[stateAlt]+math.ln(1-transProb)
viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
else:
- inferProb = currentEm[stateAlt]+ln(transProb)
- reverseProb = currentEm[stateRef]+ln(1-transProb)
+ inferProb = currentEm[stateAlt]+math.ln(transProb)
+ reverseProb = currentEm[stateRef]+math.ln(1-transProb)
viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2" )
transitFlag = false
outFileTotalCountMtx.setPosition(49)
diff --git a/sscocaller.nimble b/sscocaller.nimble
index 90dfafa..288932a 100644
--- a/sscocaller.nimble
+++ b/sscocaller.nimble
@@ -10,8 +10,8 @@ bin = @["sscocaller"]
# Dependencies
-requires "nim >= 1.4.0","docopt","hts >= 0.3.4"
-requires "https://github.com/sdwfrost/distributions.git"
+requires "nim >= 1.2.0","docopt","hts >= 0.3.4"
+requires "https://github.com/ruqianl/distributions.git"
# task test, "run the tests":
# exec "nim c -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/test_groups"
--
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