[med-svn] [picard-tools] 01/01: Adapt patches

[Andreas Tille]

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

commit 521669d08a83863d5339051fc7fc7b1fd3eef4e7
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 18 14:39:27 2016 +0100

    Adapt patches
---
 debian/patches/10-build.xml.patch              |  4 ++--
 debian/patches/30-tests-fix-dataprovider.patch | 28 ++++++++++++++++----------
 2 files changed, 19 insertions(+), 13 deletions(-)

diff --git a/debian/patches/10-build.xml.patch b/debian/patches/10-build.xml.patch
index 8d9e09b..bc3f136 100644
--- a/debian/patches/10-build.xml.patch
+++ b/debian/patches/10-build.xml.patch
@@ -38,7 +38,7 @@ Last-Updated: 2016-07-07
 -    toolVersion = "0.7.5.201505241946"
 -}
 -
- final htsjdkVersion = System.getProperty('htsjdk.version', '2.6.0')
+ final htsjdkVersion = System.getProperty('htsjdk.version', '2.8.0')
  
  dependencies {
 @@ -60,9 +38,18 @@ dependencies {
@@ -62,7 +62,7 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -321,19 +308,3 @@ task copyJavadoc(dependsOn: 'javadoc', t
+@@ -323,19 +310,3 @@ task copyJavadoc(dependsOn: 'javadoc', t
      from 'build/docs/javadoc'
      into "$htmlDir/javadoc"
  }
diff --git a/debian/patches/30-tests-fix-dataprovider.patch b/debian/patches/30-tests-fix-dataprovider.patch
index 689e611..d9100ae 100644
--- a/debian/patches/30-tests-fix-dataprovider.patch
+++ b/debian/patches/30-tests-fix-dataprovider.patch
@@ -2,28 +2,34 @@ 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 @@
+@@ -21,22 +21,22 @@ public class CollectHsMetricsTest extend
  
      @DataProvider(name = "collectHsMetricsDataProvider")
      public Object[][] targetedIntervalDataProvider() {
 -        final String referenceFile = TEST_DIR + "/chrM.fasta";
 -        final String intervals = TEST_DIR + "/chrM.interval_list";
+-        final String twoSmallIntervals = TEST_DIR + "/two-small.interval_list";
 +        final String referenceFile = TEST_DIR.getAbsolutePath() + "/chrM.fasta";
 +        final String intervals = TEST_DIR.getAbsolutePath() + "/chrM.interval_list";
++        final String twoSmallIntervals = TEST_DIR.getAbsolutePath() + "/two-small.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},
+                 // two reads, each has 100 bases. bases in one read are medium quality (20), in the other read poor quality (10).
+                 // test that we exclude half of the bases
+-                {TEST_DIR + "/lowbaseq.sam",    intervals, 1, 10, true,  2, 200, 0.5, 0.0, 0.50, 0.0,   1000},
++                {TEST_DIR.getAbsolutePath() + "/lowbaseq.sam",    intervals, 1, 10, true,  2, 200, 0.5, 0.0, 0.50, 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_DIR + "/lowmapq.sam",     intervals, 2, 0, true,  2, 202, 0,   0.0, 0.505, 0.0,   1000},
++                {TEST_DIR.getAbsolutePath() + "/lowmapq.sam",     intervals, 2, 0, true,  2, 202, 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_DIR + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 0,   0.5, 0.505, 0.505, 1000},
++                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", intervals, 0, 0, true,  2, 202, 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}
+-                {TEST_DIR + "/overlapping.sam", intervals, 0, 0, false, 2, 202, 0,   0.0, 0.505, 0.505, 1000},
++                {TEST_DIR.getAbsolutePath() + "/overlapping.sam", intervals, 0, 0, false, 2, 202, 0,   0.0, 0.505, 0.505, 1000},
+                 // A read 10 base pairs long. two intervals: one maps identically to the read, other does not overlap at all
+-                {TEST_DIR + "/single-short-read.sam", twoSmallIntervals, 20, 20, true, 1, 10, 0.0, 0.0, 0.5, 0.0, 1000 }
++                {TEST_DIR.getAbsolutePath() + "/single-short-read.sam", twoSmallIntervals, 20, 20, true, 1, 10, 0.0, 0.0, 0.5, 0.0, 1000 }
+ 
          };
      }
- 

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