From 5fa3f7ed3ab060857cd66da73f562115153186e7 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 9 Jun 2009 02:25:17 +0000
Subject: [PATCH] Added absolute path bug fix for Mark.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@949 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/RecalQual.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/python/RecalQual.py b/python/RecalQual.py
index eb70d22ab..987c5d7b2 100755
--- a/python/RecalQual.py
+++ b/python/RecalQual.py
@@ -16,6 +16,15 @@ output_root = './'
 # If editing, please end this variable with a trailing slash.
 resources='resources/'
 
+import getopt,glob,os,sys
+import LogisticRegressionByReadGroup
+
+# if the provided resources path is relative, convert it to a path
+# relative to the calling script rather than the cwd.
+if not os.path.isabs(resources):
+    application_path = os.path.dirname(sys.argv[0])
+    resources = os.path.abspath(application_path) + '/' + resources
+
 # Where does the reference live?
 reference_base = resources + 'human_b36_both'
 reference      = reference_base + '.fasta'
@@ -30,9 +39,6 @@ gatk = resources + 'gatk/GenomeAnalysisTK.jar'
 logistic_regression_script = resources + 'logistic_regression.R'
 empirical_vs_reported_grapher = resources + 'plot_q_emp_stated_hst.R'
 
-import getopt,glob,os,sys
-import LogisticRegressionByReadGroup
-
 def exit(msg,errorcode):
     print msg
     sys.exit(errorcode)
@@ -122,6 +128,8 @@ do_recalibration = not (evaluate_requested and not recalibrate_requested)
 # Only evaluate if the user specifically requested evaluation.
 do_evaluation = evaluate_requested
 
+print 'Looking for supplemental files in ' + resources
+
 # check that the input bam file exists, and that the bam is indexed.
 bam = args[0]
 bam_index = bam + '.bai'