From e45b699ac059045f4e762c42b872c42eaf250fb3 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Feb 2011 16:19:58 +0000
Subject: [PATCH] standardizing the name of the scripts and fixing some bugs
 with the remapping.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5245 348d0f76-0448-11de-a6fe-93d51630548a
---
 lua/{MergeIntervals.lua => mergeIntervals.lua} | 0
 lua/remapAmplicons.lua                         | 1 +
 2 files changed, 1 insertion(+)
 rename lua/{MergeIntervals.lua => mergeIntervals.lua} (100%)

diff --git a/lua/MergeIntervals.lua b/lua/mergeIntervals.lua
similarity index 100%
rename from lua/MergeIntervals.lua
rename to lua/mergeIntervals.lua
diff --git a/lua/remapAmplicons.lua b/lua/remapAmplicons.lua
index c858b01bf..df20cfa27 100644
--- a/lua/remapAmplicons.lua
+++ b/lua/remapAmplicons.lua
@@ -53,6 +53,7 @@ local function processSamHeaderLine(l, amplicons)
     if not header.sq then header.sq = {} end
     local ampName = l:match("@SQ%s+SN:ps%d+_([%w%p_]+).*")
     local chr = amplicons[ampName].chr
+print("DEBUG: ", ampName, chr)
     header.sq[chr] = chrlength[chr]
   end
 end