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this -1 made ALL the difference in the world. Minor bug fix. 

Regular updates to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-11 19:25:09 +00:00
parent cdf53188d6
commit 50c2fa3c3a
2 changed files with 3 additions and 7 deletions
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4
lua/remapAmplicons.lua
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@ -3,6 +3,8 @@ local samFile = arg[2]
local headerFile = io.open(arg[2]:match("(.*).sam")..".header.sam", "w") local headerFile = io.open(arg[2]:match("(.*).sam")..".header.sam", "w")
local bodyFile = io.open(arg[2]:match("(.*).sam")..".body.sam", "w") local bodyFile = io.open(arg[2]:match("(.*).sam")..".body.sam", "w")
-- These sizes are hardcoded for hg19, but future versions of this script should optionally take a .fai file to build this table.
chrlength = {} chrlength = {}
chrlength["1"] =249250621 chrlength["1"] =249250621
chrlength["2"] =243199373 chrlength["2"] =243199373
@ -76,7 +78,7 @@ for l in io.lines(samFile) do
if l:sub(1,1) == "@" then processSamHeaderLine(l, amplicons) if l:sub(1,1) == "@" then processSamHeaderLine(l, amplicons)
else else
local before, amp, mapStart, after = l:match("(%d+%s+%d+%s+)ps%d+_([%w%p_]+)%s+(%d+)(.*)") local before, amp, mapStart, after = l:match("(%d+%s+%d+%s+)ps%d+_([%w%p_]+)%s+(%d+)(.*)")
table.insert(reads, before..amplicons[amp].chr.."\t"..amplicons[amp].startPos + mapStart..after) table.insert(reads, before..amplicons[amp].chr.."\t"..amplicons[amp].startPos + mapStart - 1 ..after)
end end
end end

6
scala/qscript/oneoffs/carneiro/pbCalling.scala
View File

@ -17,8 +17,6 @@ class pbCalling extends QScript {
@Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false) @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
var noBAQ: Boolean = false var noBAQ: Boolean = false
@Argument(shortName="noMASK", doc="turns off MASK calculation", required=false)
var noMASK: Boolean = false
@ -184,10 +182,6 @@ class pbCalling extends QScript {
this.filterName ++= List("HARD_TO_VALIDATE") this.filterName ++= List("HARD_TO_VALIDATE")
this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"") this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
this.analysisName = t.name + "_VF" this.analysisName = t.name + "_VF"
if (!noMASK) {
this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
this.maskName = "InDel"
}
} }
// 3.) VQSR part1 Generate Gaussian clusters based on truth sites // 3.) VQSR part1 Generate Gaussian clusters based on truth sites