This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository picard-tools.
commit 521669d08a83863d5339051fc7fc7b1fd3eef4e7 Author: Andreas Tille <[email protected]> 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 <[email protected]> --- 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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