[med-svn] [htsjdk] 03/03: new upstream version
Andreas Tille
tille at debian.org
Sat Sep 10 07:24:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit 191617e0a9605c1ee852f47cfaf046ea81999227
Author: Andreas Tille <tille at debian.org>
Date: Sat Sep 10 08:10:03 2016 +0200
new upstream version
---
debian/changelog | 6 ++
debian/patches/13-skip_network_tests | 172 ++++++++++++++++++-----------------
2 files changed, 93 insertions(+), 85 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 259e9ed..441c5f2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+htsjdk (2.6.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sat, 10 Sep 2016 08:03:30 +0200
+
htsjdk (2.5.0+dfsg.2-2) unstable; urgency=medium
[ Vincent Danjean ]
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index e77ff4e..c326879 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -55,8 +55,8 @@ Last-Updated: 2015-01-06
}
--- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
+++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-@@ -26,86 +26,4 @@ public class AbstractFeatureReaderTest {
- final static String HTTP_INDEXED_VCF_PATH = "http://www.broadinstitute.org/~picard/testdata/ex2.vcf";
+@@ -27,86 +27,4 @@ public class AbstractFeatureReaderTest {
+ final static String HTTP_INDEXED_VCF_PATH = TestUtil.BASE_URL_FOR_HTTP_TESTS + "ex2.vcf";
final static String LOCAL_MIRROR_HTTP_INDEXED_VCF_PATH = VariantBaseTest.variantTestDataRoot + "ex2.vcf";
- /**
@@ -293,7 +293,7 @@ Last-Updated: 2015-01-06
}
--- a/src/test/java/htsjdk/samtools/sra/SRATest.java
+++ b/src/test/java/htsjdk/samtools/sra/SRATest.java
-@@ -57,376 +57,4 @@ import java.util.TreeSet;
+@@ -57,378 +57,4 @@ import java.util.TreeSet;
*/
public class SRATest extends AbstractSRATest {
@@ -341,13 +341,8 @@ Last-Updated: 2015-01-06
- @DataProvider(name = "testGroups")
- private Object[][] createDataForGroups() {
- return new Object[][] {
-- {"SRR822962", new TreeSet<>(Arrays.asList(
-- "GS54389-FS3-L08", "GS57511-FS3-L08", "GS54387-FS3-L02", "GS54387-FS3-L01",
-- "GS57510-FS3-L01", "GS57510-FS3-L03", "GS54389-FS3-L07", "GS54389-FS3-L05",
-- "GS54389-FS3-L06", "GS57510-FS3-L02", "GS57510-FS3-L04", "GS54387-FS3-L03",
-- "GS46253-FS3-L03"))
-- },
-- {"SRR2096940", new HashSet<>(Arrays.asList("SRR2096940"))}
+- {"SRR1035115", new TreeSet<>(Arrays.asList("15656144_B09YG", "15656144_B09MR"))},
+- {"SRR2096940", new TreeSet<>(Arrays.asList("SRR2096940"))}
- };
- }
-
@@ -388,15 +383,17 @@ Last-Updated: 2015-01-06
- private Object[][] createDataForReferences() {
- return new Object[][] {
- // primary alignment only
-- {"SRR1063272", 1,
-- Arrays.asList("supercont2.1", "supercont2.2", "supercont2.3", "supercont2.4",
-- "supercont2.5", "supercont2.6", "supercont2.7", "supercont2.8",
-- "supercont2.9", "supercont2.10", "supercont2.11", "supercont2.12",
-- "supercont2.13", "supercont2.14"),
-- Arrays.asList(2291499, 1621675, 1575141, 1084805,
-- 1814975, 1422463, 1399503, 1398693,
-- 1186808, 1059964, 1561994, 774062,
-- 756744, 926563)},
+- {"SRR353866", 9,
+- Arrays.asList(
+- "AAAB01001871.1", "AAAB01002233.1", "AAAB01004056.1", "AAAB01006027.1",
+- "AAAB01008846.1", "AAAB01008859.1", "AAAB01008960.1", "AAAB01008982.1",
+- "AAAB01008987.1"
+- ),
+- Arrays.asList(
+- 1115, 1034, 1301, 1007,
+- 11308833, 12516315, 23099915, 1015562,
+- 16222597
+- )},
- };
- }
-
@@ -448,67 +445,66 @@ Last-Updated: 2015-01-06
- private Object[][] createDataForRowsTest() {
- return new Object[][] {
- // primary alignment only
-- {"SRR1063272", 0, 99, "SRR1063272.R.1",
-- "ACTCGACATTCTGCCTTCGACCTATCTTTCTCCTCTCCCAGTCATCGCCCAGTAGAATTACCAGGCAATGAACCAGGGCCTTCCATCCCAACGGCACAGCA",
-- "@@CDDBDFFBFHFIEEFGIGGHIEHIGIGGFGEGAFDHIIIIIGGGDFHII;=BF at FEHGIEEH?AHHFHFFFFDC5'5=?CC?ADCD at AC??9BDDCDB<",
-- 86, "101M", "supercont2.1", 60, true, false},
+- {"SRR2127895", 1, 83, "SRR2127895.R.1",
+- "CGTGCGCGTGACCCATCAGATGCTGTTCAATCAGTGGCAAATGCGGAACGGTTTCTGCGGGTTGCCGATATTCTGGAGAGTAATGCCAGGCAGGGGCAGGT",
+- "DDBDDDDDBCABC at CCDDDC?99CCA:CDCDDDDDDDECDDDFFFHHHEGIJIIGIJIHIGJIJJJJJJJIIJIIHIGJIJJJIJJIHFFBHHFFFDFBBB",
+- 366, "29S72M", "gi|152968582|ref|NC_009648.1|", 147, true, false, false},
-
- // small SRA archive
- {"SRR2096940", 1, 16, "SRR2096940.R.3",
- "GTGTGTCACCAGATAAGGAATCTGCCTAACAGGAGGTGTGGGTTAGACCCAATATCAGGAGACCAGGAAGGAGGAGGCCTAAGGATGGGGCTTTTCTGTCACCAATCCTGTCCCTAGTGGCCCCACTGTGGGGTGGAGGGGACAGATAAAAGTACCCAGAACCAGAG",
- "AAAABFFFFFFFGGGGGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIII7IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGFGFFDFFFFFC",
-- 55627016, "167M", "CM000681.1", 42, false, false},
+- 55627016, "167M", "CM000681.1", 42, false, false, false},
-
- {"SRR2096940", 10591, 4, "SRR2096940.R.10592",
- "CTCTGGTTCTGGGTACTTTTATCTGTCCCCTCCACCCCACAGTGGCGAGCCAGATTCCTTATCTGGTGACACAC",
- "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII",
-- -1, null, null, -1, false, false},
+- -1, null, null, -1, false, false, false},
-
- // primary and secondary alignments
- {"SRR833251", 81, 393, "SRR833251.R.51",
- "ATGCAAATCCGAATGGGCTATTTGTGGGTACTTGGGCAGGTAAGTAGCTGGCAATCTTGGTCGGTAAACCAATACCCAAGTTCACATAGGCACCATCGGGA",
- "CCCFFFFFHHHHHIJJJIJJJJJIIJJJGIJIJIIJIJJJDGIGIIJIJIHIJJJJJJGIGHIHEDFFFFDDEEEDDDDDCDEEDDDDDDDDDDDDDBBDB",
-- 1787186, "38M63S", "gi|169794206|ref|NC_010410.1|", 11, true, true},
+- 1787186, "38M63S", "gi|169794206|ref|NC_010410.1|", 11, true, true, true},
-
- // local SRA file
- {"src/test/resources/htsjdk/samtools/sra/test_archive.sra", 1, 99, "test_archive.R.2",
- "TGTCGATGCTGAAAGTGTCTGCGGTGAACCACTTCATGCACAGCGCACACTGCAGCTCCACTTCACCCAGCTGACGGCCGTTCTCATCGTCTCCAGAGCCCGTCTGAGCGTCCGCTGCTTCAGAACTGTCCCCGGCTGTATCCTGAAGAC",
- "BBAABBBFAFFFGGGGGGGGGGGGEEFHHHHGHHHHHFHHGHFDGGGGGHHGHHHHHHHHHHHHFHHHGHHHHHHGGGGGGGHGGHHHHHHHHHGHHHHHGGGGHGHHHGGGGGGGGGHHHHEHHHHHHHHHHGCGGGHHHHHHGBFFGF",
-- 2811570, "150M", "NC_007121.5", 60, true, false}
+- 2811570, "150M", "NC_007121.5", 60, true, false, false}
- };
- }
-
- @Test(dataProvider = "testRows")
- public void testRows(String acc, int recordIndex, int flags, String readName, String bases, String quals, int refStart, String cigar,
-- String refName, int mapQ, boolean hasMate, boolean isSecondaryAlignment) {
+- String refName, int mapQ, boolean hasMate, boolean isSecondOfPair, boolean isSecondaryAlignment) {
- SAMRecord record = getRecordByIndex(acc, recordIndex, false);
-
-- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
+- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondOfPair, isSecondaryAlignment);
- }
-
- @Test(dataProvider = "testRows")
- public void testRowsAfterIteratorDetach(String acc, int recordIndex, int flags, String readName, String bases, String quals,
- int refStart, String cigar, String refName, int mapQ, boolean hasMate,
-- boolean isSecondaryAlignment) {
+- boolean isSecondOfPair, boolean isSecondaryAlignment) {
- SAMRecord record = getRecordByIndex(acc, recordIndex, true);
-
-- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
+- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondOfPair, isSecondaryAlignment);
- }
-
- @Test(dataProvider = "testRows")
- public void testRowsOverrideValues(String acc, int recordIndex, int flags, String readName, String bases, String quals,
- int refStart, String cigar, String refName, int mapQ, boolean hasMate,
-- boolean isSecondaryAlignment) {
+- boolean isSecondOfPair, boolean isSecondaryAlignment) {
- SAMRecord record = getRecordByIndex(acc, recordIndex, true);
- SAMFileHeader header = record.getHeader();
-
--
- record.setFlags(0);
- record.setReadUnmappedFlag(refStart == -1);
- record.setReadBases("C".getBytes());
- record.setBaseQualities(SAMUtils.fastqToPhred("A"));
- if (refStart == -1) {
-- checkSAMRecord(record, 4, readName, "C", "A", refStart, "1M", refName, mapQ, false, false);
+- checkSAMRecord(record, 4, readName, "C", "A", refStart, "1M", refName, mapQ, false, false, false);
- } else {
- int sequenceIndex = header.getSequenceIndex(refName);
- Assert.assertFalse(sequenceIndex == -1);
@@ -528,14 +524,14 @@ Last-Updated: 2015-01-06
- record.setMappingQuality(mapQ - 1);
- record.setReferenceIndex(sequenceIndex);
-
-- checkSAMRecord(record, 0, readName, "C", "A", refStart - 100, "1M", refName, mapQ - 1, false, false);
+- checkSAMRecord(record, 0, readName, "C", "A", refStart - 100, "1M", refName, mapQ - 1, false, false, false);
- }
- }
-
- @Test(dataProvider = "testRows")
- public void testRowsBySpan(String acc, int recordIndex, int flags, String readName, String bases, String quals,
- int refStart, String cigar, String refName, int mapQ, boolean hasMate,
-- boolean isSecondaryAlignment) {
+- boolean isSecondOfPair, boolean isSecondaryAlignment) {
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -570,13 +566,13 @@ Last-Updated: 2015-01-06
- }
- }
-
-- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
+- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondOfPair, isSecondaryAlignment);
- }
-
- @Test(dataProvider = "testRows")
- public void testRowsByIndex(String acc, int recordIndex, int flags, String readName, String bases, String quals,
- int refStart, String cigar, String refName, int mapQ, boolean hasMate,
-- boolean isSecondaryAlignment) {
+- boolean isSecondOfPair, boolean isSecondaryAlignment) {
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -606,13 +602,15 @@ Last-Updated: 2015-01-06
- continue;
- }
-
-- if (currentRecord.getReadName().equals(readName)) {
+- if (currentRecord.getReadName().equals(readName)
+- && currentRecord.getNotPrimaryAlignmentFlag() == isSecondaryAlignment
+- && (!hasMate || currentRecord.getSecondOfPairFlag() == isSecondOfPair)) {
- record = currentRecord;
- break;
- }
- }
-
-- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
+- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondOfPair, isSecondaryAlignment);
- }
-
- private SAMRecord getRecordByIndex(String acc, int recordIndex, boolean detach) {
@@ -641,7 +639,7 @@ Last-Updated: 2015-01-06
-
- private void checkSAMRecord(SAMRecord record, int flags, String readName, String bases, String quals,
- int refStart, String cigar, String refName, int mapQ, boolean hasMate,
-- boolean isSecondaryAlignment) {
+- boolean isSecondOfPair, boolean isSecondaryAlignment) {
-
- Assert.assertNotNull(record, "Record with read id: " + readName + " was not found by span created from index");
-
@@ -649,11 +647,15 @@ Last-Updated: 2015-01-06
- Assert.assertNull(validationErrors, "SRA Lazy record is invalid. List of errors: " +
- (validationErrors != null ? validationErrors.toString() : ""));
-
+- Assert.assertEquals(record.getReadName(), readName);
- Assert.assertEquals(new String(record.getReadBases()), bases);
- Assert.assertEquals(record.getBaseQualityString(), quals);
- Assert.assertEquals(record.getReadPairedFlag(), hasMate);
- Assert.assertEquals(record.getFlags(), flags);
- Assert.assertEquals(record.getNotPrimaryAlignmentFlag(), isSecondaryAlignment);
+- if (hasMate) {
+- Assert.assertEquals(record.getSecondOfPairFlag(), isSecondOfPair);
+- }
- if (refStart == -1) {
- Assert.assertEquals(record.getReadUnmappedFlag(), true);
- Assert.assertEquals(record.getAlignmentStart(), 0);
@@ -670,36 +672,6 @@ Last-Updated: 2015-01-06
- }
-
}
---- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
-+++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
-@@ -135,27 +135,4 @@ public class TabixReaderTest {
-
- }
-
-- /**
-- * Test reading a tabix file over http
-- *
-- * @throws java.io.IOException
-- */
-- @Test
-- public void testRemoteQuery() throws IOException {
-- String tabixFile = "http://www.broadinstitute.org/~picard/testdata/igvdata/tabix/trioDup.vcf.gz";
--
-- TabixReader tabixReader = new TabixReader(tabixFile);
--
-- TabixIteratorLineReader lineReader = new TabixIteratorLineReader(
-- tabixReader.query(tabixReader.chr2tid("4"), 320, 330));
--
-- int nRecords = 0;
-- String nextLine;
-- while ((nextLine = lineReader.readLine()) != null) {
-- assertTrue(nextLine.startsWith("4"));
-- nRecords++;
-- }
-- assertTrue(nRecords > 0);
--
-- }
- }
--- a/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
+++ b/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
@@ -14,18 +14,4 @@ import static org.testng.Assert.assertTr
@@ -1020,13 +992,55 @@ Last-Updated: 2015-01-06
}
+--- a/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
++++ b/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
+@@ -7,9 +7,4 @@ import java.io.IOException;
+
+ public class EnaRefServiceTest {
+
+- @Test
+- public void test() throws IOException, EnaRefService.GaveUpException {
+- Assert.assertNotNull(new EnaRefService().getSequence("57151e6196306db5d9f33133572a5482"));
+- Assert.assertNotNull(new EnaRefService().getSequence("0000088cbcebe818eb431d58c908c698"));
+- }
+ }
+--- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
++++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
+@@ -136,27 +136,4 @@ public class TabixReaderTest {
+
+ }
+
+- /**
+- * Test reading a tabix file over http
+- *
+- * @throws java.io.IOException
+- */
+- @Test
+- public void testRemoteQuery() throws IOException {
+- String tabixFile = TestUtil.BASE_URL_FOR_HTTP_TESTS +"igvdata/tabix/trioDup.vcf.gz";
+-
+- TabixReader tabixReader = new TabixReader(tabixFile);
+-
+- TabixIteratorLineReader lineReader = new TabixIteratorLineReader(
+- tabixReader.query(tabixReader.chr2tid("4"), 320, 330));
+-
+- int nRecords = 0;
+- String nextLine;
+- while ((nextLine = lineReader.readLine()) != null) {
+- assertTrue(nextLine.startsWith("4"));
+- nRecords++;
+- }
+- assertTrue(nRecords > 0);
+-
+- }
+ }
--- a/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
+++ b/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
-@@ -42,285 +42,7 @@ import static org.testng.Assert.*;
+@@ -43,285 +43,7 @@ import static org.testng.Assert.*;
public class BAMRemoteFileTest {
private final File BAM_INDEX_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai");
private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
-- private final String BAM_URL_STRING = "http://www.broadinstitute.org/~picard/testdata/index_test.bam";
+- private final String BAM_URL_STRING = TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam";
- private final URL bamURL;
private final boolean mVerbose = false;
@@ -1308,15 +1322,3 @@ Last-Updated: 2015-01-06
- }
- }
}
---- a/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
-+++ b/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
-@@ -7,9 +7,4 @@ import java.io.IOException;
-
- public class EnaRefServiceTest {
-
-- @Test
-- public void test() throws IOException, EnaRefService.GaveUpException {
-- Assert.assertNotNull(new EnaRefService().getSequence("57151e6196306db5d9f33133572a5482"));
-- Assert.assertNotNull(new EnaRefService().getSequence("0000088cbcebe818eb431d58c908c698"));
-- }
- }
--
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