From 50c2fa3c3a25ee9442bc91f6c018816dd0c4419b Mon Sep 17 00:00:00 2001 From: carneiro Date: Fri, 11 Feb 2011 19:25:09 +0000 Subject: [PATCH] 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 --- lua/remapAmplicons.lua | 4 +++- scala/qscript/oneoffs/carneiro/pbCalling.scala | 6 ------ 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/lua/remapAmplicons.lua b/lua/remapAmplicons.lua index f70748129..c858b01bf 100644 --- a/lua/remapAmplicons.lua +++ b/lua/remapAmplicons.lua @@ -3,6 +3,8 @@ local samFile = arg[2] local headerFile = io.open(arg[2]:match("(.*).sam")..".header.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["1"] =249250621 chrlength["2"] =243199373 @@ -76,7 +78,7 @@ for l in io.lines(samFile) do if l:sub(1,1) == "@" then processSamHeaderLine(l, amplicons) else 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 diff --git a/scala/qscript/oneoffs/carneiro/pbCalling.scala b/scala/qscript/oneoffs/carneiro/pbCalling.scala index 614809f09..ee1d29a55 100755 --- a/scala/qscript/oneoffs/carneiro/pbCalling.scala +++ b/scala/qscript/oneoffs/carneiro/pbCalling.scala @@ -17,8 +17,6 @@ class pbCalling extends QScript { @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=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.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"") 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