[med-svn] [picard-tools] 01/01: make data provider match test method to fix test

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository picard-tools.

commit cd4d777b4bd57634d86a1c58fb9309311e3017da
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Sep 10 15:53:29 2016 +0000

    make data provider match test method to fix test
---
 debian/patches/30-tests-fix-dataprovider.patch | 29 ++++++++++++++++++++++++++
 debian/patches/series                          |  1 +
 2 files changed, 30 insertions(+)

diff --git a/debian/patches/30-tests-fix-dataprovider.patch b/debian/patches/30-tests-fix-dataprovider.patch
new file mode 100644
index 0000000..689e611
--- /dev/null
+++ b/debian/patches/30-tests-fix-dataprovider.patch
@@ -0,0 +1,29 @@
+Description: fix data provider requirements
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
++++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java
+@@ -20,18 +20,18 @@
+ 
+     @DataProvider(name = "collectHsMetricsDataProvider")
+     public Object[][] targetedIntervalDataProvider() {
+-        final String referenceFile = TEST_DIR + "/chrM.fasta";
+-        final String intervals = TEST_DIR + "/chrM.interval_list";
++        final String referenceFile = TEST_DIR.getAbsolutePath() + "/chrM.fasta";
++        final String intervals = TEST_DIR.getAbsolutePath() + "/chrM.interval_list";
+ 
+         return new Object[][] {
+                 // test that all bases (read 2) with base quality 1 are filtered out
+-                {TEST_DIR + "/lowbaseq.sam",    referenceFile, intervals, "NONE", 1, 1, true,  2, 202, 0.5, 0.0, 0.505, 0.0,   1000},
++                {TEST_DIR.getAbsolutePath() + "/lowbaseq.sam",    referenceFile, intervals, "NONE", 1, 1, true,  2, 202, 0.5,   0.0, 0.505, 0.0,   1000},
+                 // test that read 2 (with mapping quality 1) is filtered out with minimum mapping quality 2
+-                {TEST_DIR + "/lowmapq.sam",     referenceFile, intervals, "NONE", 2, 0, true,  2, 202, 0,   0.0, 0.505, 0.0,   1000},
++                {TEST_DIR.getAbsolutePath() + "/lowmapq.sam",     referenceFile, intervals, "NONE", 2, 0, true,  2, 202, 0.0,   0.0, 0.505, 0.0,   1000},
+                 // test that we clip overlapping bases
+-                {TEST_DIR + "/overlapping.sam", referenceFile, intervals, "NONE", 0, 0, true,  2, 202, 0,   0.5, 0.505, 0.505, 1000},
++                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", referenceFile, intervals, "NONE", 0, 0, true,  2, 202, 0.0,   0.5, 0.505, 0.505, 1000},
+                 // test that we do not clip overlapping bases
+-                {TEST_DIR + "/overlapping.sam", referenceFile, intervals, "NONE", 0, 0, false, 2, 202, 0,   0.0, 0.505, 0.505, 1000}
++                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", referenceFile, intervals, "NONE", 0, 0, false, 2, 202, 0.0,   0.0, 0.505, 0.505, 1000}
+         };
+     }
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 1eb1076..5267fe2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 10-build.xml.patch
 20-shadowjar.patch
+30-tests-fix-dataprovider.patch

-- 
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