[med-svn] [htsjdk] 04/06: Update patches
Vincent Danjean
vdanjean at debian.org
Mon Mar 14 20:11:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a commit to branch master
in repository htsjdk.
commit 684a7cbbe503fa2464db079de811f093e14fc491
Author: Vincent Danjean <Vincent.Danjean at ens-lyon.org>
Date: Mon Mar 14 16:49:09 2016 +0100
Update patches
---
debian/patches/10-build.xml | 16 +-
debian/patches/13-skip_network_tests | 319 ++++++++++++++---------------------
2 files changed, 141 insertions(+), 194 deletions(-)
diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml
index b9e29ab..d5e6622 100644
--- a/debian/patches/10-build.xml
+++ b/debian/patches/10-build.xml
@@ -13,7 +13,7 @@ Forwarded: no
- <property name="repository.revision" value=""/>
+ <property name="repository.revision" value="dfsg"/>
- <property name="htsjdk-version" value="2.0.1"/>
+ <property name="htsjdk-version" value="2.1.1"/>
<property name="htsjdk-version-file" value="htsjdk.version.properties"/>
<property name="testng.verbosity" value="2"/>
@@ -72,6 +72,12 @@
@@ -29,15 +29,23 @@ Forwarded: no
</path>
</target>
-@@ -128,6 +134,7 @@
+@@ -132,6 +138,7 @@
+ <pathelement path="${classes}"/>
+ <pathelement path="${classes.test}"/>
+ <pathelement path="${scripts}"/>
++ <pathelement path="/usr/share/java/jcommander.jar"/>
+ </classpath>
+ <classfileset dir="${classes.test}">
+ <include name="**/Test*.class"/>
+@@ -176,6 +183,7 @@
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
+ <pathelement path="/usr/share/java/jcommander.jar"/>
</classpath>
<classfileset dir="${classes.test}">
- <include name="**/Test*.class"/>
-@@ -204,8 +211,14 @@
+ <include name="**/${name}.class"/>
+@@ -218,8 +226,14 @@
<fileset dir="${lib}">
<include name="**/*.jar" />
</fileset>
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index 49d7341..8a7a562 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -147,34 +147,138 @@ Last-Updated: 2015-01-06
@Test
public void testSkip() throws IOException {
+--- a/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
++++ b/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
+@@ -50,85 +50,4 @@
+ private static final int LAST_BIN_LEVEL = GenomicIndexUtil.LEVEL_STARTS.length - 1;
+ private static final int SRA_BIN_OFFSET = GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL];
+
+- @Test
+- public void testLevelSize() {
+- final SRAIndex index = getIndex(DEFAULT_ACCESSION);
+- Assert.assertEquals(index.getLevelSize(0), GenomicIndexUtil.LEVEL_STARTS[1] - GenomicIndexUtil.LEVEL_STARTS[0]);
+-
+- Assert.assertEquals(index.getLevelSize(LAST_BIN_LEVEL), GenomicIndexUtil.MAX_BINS - GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL] - 1);
+- }
+-
+- @Test
+- public void testLevelForBin() {
+- final SRAIndex index = getIndex(DEFAULT_ACCESSION);
+- final Bin bin = new Bin(0, SRA_BIN_OFFSET);
+- Assert.assertEquals(index.getLevelForBin(bin), LAST_BIN_LEVEL);
+- }
+-
+- @DataProvider(name = "testBinLocuses")
+- private Object[][] createDataForBinLocuses() {
+- return new Object[][] {
+- {DEFAULT_ACCESSION, 0, 0, 1, SRAIndex.SRA_BIN_SIZE},
+- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 2}
+- };
+- }
+-
+- @Test(dataProvider = "testBinLocuses")
+- public void testBinLocuses(SRAAccession acc, int reference, int binIndex, int firstLocus, int lastLocus) {
+- final SRAIndex index = getIndex(acc);
+- final Bin bin = new Bin(reference, SRA_BIN_OFFSET + binIndex);
+-
+- Assert.assertEquals(index.getFirstLocusInBin(bin), firstLocus);
+- Assert.assertEquals(index.getLastLocusInBin(bin), lastLocus);
+- }
+-
+- @DataProvider(name = "testBinOverlappings")
+- private Object[][] createDataForBinOverlappings() {
+- return new Object[][] {
+- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE, new HashSet<>(Arrays.asList(0))},
+- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 2, new HashSet<>(Arrays.asList(1))},
+- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 3, new HashSet<>(Arrays.asList(1, 2))},
+- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE * 2, SRAIndex.SRA_BIN_SIZE * 2 + 1, new HashSet<>(Arrays.asList(1, 2))}
+- };
+- }
+-
+-
+- @Test(dataProvider = "testBinOverlappings")
+- public void testBinOverlappings(SRAAccession acc, int reference, int firstLocus, int lastLocus, Set<Integer> binNumbers) {
+- final SRAIndex index = getIndex(acc);
+- final Iterator<Bin> binIterator = index.getBinsOverlapping(reference, firstLocus, lastLocus).iterator();
+- final Set<Integer> binNumbersFromIndex = new HashSet<>();
+- while (binIterator.hasNext()) {
+- final Bin bin = binIterator.next();
+- binNumbersFromIndex.add(bin.getBinNumber() - SRA_BIN_OFFSET);
+- }
+-
+- Assert.assertEquals(binNumbers, binNumbersFromIndex);
+- }
+-
+- @DataProvider(name = "testSpanOverlappings")
+- private Object[][] createDataForSpanOverlappings() {
+- return new Object[][] {
+- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE, new long[] {0, SRAIndex.SRA_CHUNK_SIZE} },
+- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE * 2, SRAIndex.SRA_BIN_SIZE * 2 + 1, new long[]{0, SRAIndex.SRA_CHUNK_SIZE} },
+- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE + 1, new long[]{0, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE * 2} },
+- };
+- }
+-
+- @Test(dataProvider = "testSpanOverlappings")
+- public void testSpanOverlappings(SRAAccession acc, int reference, int firstLocus, int lastLocus, long[] spanCoordinates) {
+- final SRAIndex index = getIndex(acc);
+- final BAMFileSpan span = index.getSpanOverlapping(reference, firstLocus, lastLocus);
+-
+- long[] coordinatesFromIndex = span.toCoordinateArray();
+-
+- Assert.assertTrue(Arrays.equals(coordinatesFromIndex, spanCoordinates),
+- "Coordinates mismatch. Expected: " + Arrays.toString(spanCoordinates) +
+- " but was : " + Arrays.toString(coordinatesFromIndex));
+- }
+-
+- private SRAIndex getIndex(SRAAccession acc) {
+- final SRAFileReader reader = new SRAFileReader(acc);
+- return (SRAIndex) reader.getIndex();
+- }
+ }
+--- a/build.xml
++++ b/build.xml
+@@ -141,6 +141,15 @@
+ </classpath>
+ <classfileset dir="${classes.test}">
+ <include name="**/Test*.class"/>
++ <exclude name="**/BAM*.class"/>
++ <exclude name="**/CRAM*.class"/>
++ <exclude name="**/SAM*.class"/>
++ <exclude name="**/Sam*.class"/>
++ <exclude name="**/Tabix*.class"/>
++ <exclude name="**/SRA*.class"/>
++ <exclude name="**/*FTP*.class"/>
++ <exclude name="**/EnaRef*.class"/>
++ <exclude name="**/IupacTest*.class"/>
+ <include name="**/*Test.class"/>
+ </classfileset>
+ <jvmarg value="-Xmx2G"/>
--- a/src/tests/java/htsjdk/samtools/sra/SRATest.java
+++ b/src/tests/java/htsjdk/samtools/sra/SRATest.java
-@@ -43,422 +43,4 @@
+@@ -57,375 +57,4 @@
*/
- public class SRATest {
+ public class SRATest extends AbstractSRATest {
- @DataProvider(name = "testCounts")
-- public Object[][] createDataForCounts() {
+- private Object[][] createDataForCounts() {
- return new Object[][] {
- {"SRR2096940", 10591, 498}
- };
- }
-
- @Test(dataProvider = "testCounts")
-- public void testCounts(String acc, int numberAlignments, int numberUnalignments) {
-- if (!SRAAccession.isSupported()) return;
--
+- public void testCounts(String acc, int expectedNumMapped, int expectedNumUnmapped) {
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
-
- final SAMRecordIterator samRecordIterator = reader.iterator();
-
-- checkAlignedUnalignedCountsByIterator(samRecordIterator, numberAlignments, numberUnalignments);
+- assertCorrectCountsOfMappedAndUnmappedRecords(samRecordIterator, expectedNumMapped, expectedNumUnmapped);
- }
-
- @DataProvider(name = "testCountsBySpan")
-- public Object[][] createDataForCountsBySpan() {
+- private Object[][] createDataForCountsBySpan() {
- return new Object[][] {
- {"SRR2096940", Arrays.asList(new Chunk(0, 59128983), new Chunk(59128983, 59141089)), 10591, 498},
- {"SRR2096940", Arrays.asList(new Chunk(0, 29128983), new Chunk(29128983, 59141089)), 10591, 498},
@@ -185,35 +289,31 @@ Last-Updated: 2015-01-06
- }
-
- @Test(dataProvider = "testCountsBySpan")
-- public void testCountsBySpan(String acc, List<Chunk> chunks, int numberAlignments, int numberUnalignments) {
-- if (!SRAAccession.isSupported()) return;
--
+- public void testCountsBySpan(String acc, List<Chunk> chunks, int expectedNumMapped, int expectedNumUnmapped) {
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
-
- final SAMRecordIterator samRecordIterator = ((SamReader.Indexing) reader).iterator(new BAMFileSpan(chunks));
-
-- checkAlignedUnalignedCountsByIterator(samRecordIterator, numberAlignments, numberUnalignments);
+- assertCorrectCountsOfMappedAndUnmappedRecords(samRecordIterator, expectedNumMapped, expectedNumUnmapped);
- }
-
- @DataProvider(name = "testGroups")
-- public Object[][] createDataForGroups() {
+- private Object[][] createDataForGroups() {
- return new Object[][] {
-- {"SRR822962", new TreeSet<String>(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"))
+- {"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<String>(Arrays.asList("SRR2096940"))}
+- {"SRR2096940", new HashSet<>(Arrays.asList("SRR2096940"))}
- };
- }
-
- @Test(dataProvider = "testGroups")
- public void testGroups(String acc, Set<String> groups) {
-- if (!SRAAccession.isSupported()) return;
--
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -221,7 +321,7 @@ Last-Updated: 2015-01-06
- final SAMRecordIterator samRecordIterator = reader.iterator();
-
- SAMFileHeader header = reader.getFileHeader();
-- Set<String> headerGroups = new TreeSet<String>();
+- Set<String> headerGroups = new TreeSet<>();
- for (SAMReadGroupRecord group : header.getReadGroups()) {
- Assert.assertEquals(group.getReadGroupId(), group.getId());
- headerGroups.add(group.getReadGroupId());
@@ -229,7 +329,7 @@ Last-Updated: 2015-01-06
-
- Assert.assertEquals(groups, headerGroups);
-
-- Set<String> foundGroups = new TreeSet<String>();
+- Set<String> foundGroups = new TreeSet<>();
-
- for (int i = 0; i < 10000; i++) {
- if (!samRecordIterator.hasNext()) {
@@ -246,7 +346,7 @@ Last-Updated: 2015-01-06
- }
-
- @DataProvider(name = "testReferences")
-- public Object[][] createDataForReferences() {
+- private Object[][] createDataForReferences() {
- return new Object[][] {
- // primary alignment only
- {"SRR1063272", 1,
@@ -263,8 +363,6 @@ Last-Updated: 2015-01-06
-
- @Test(dataProvider = "testReferences")
- public void testReferences(String acc, int numberFirstReferenceFound, List<String> references, List<Integer> refLengths) {
-- if (!SRAAccession.isSupported()) return;
--
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -272,7 +370,7 @@ Last-Updated: 2015-01-06
- final SAMRecordIterator samRecordIterator = reader.iterator();
-
- SAMFileHeader header = reader.getFileHeader();
-- Set<String> headerRefNames = new TreeSet<String>();
+- Set<String> headerRefNames = new TreeSet<>();
-
- for (SAMSequenceRecord ref : header.getSequenceDictionary().getSequences()) {
- String refName = ref.getSequenceName();
@@ -285,9 +383,9 @@ Last-Updated: 2015-01-06
- headerRefNames.add(refName);
- }
-
-- Assert.assertEquals(new TreeSet<String>(references), headerRefNames);
+- Assert.assertEquals(new TreeSet<>(references), headerRefNames);
-
-- Set<String> foundRefNames = new TreeSet<String>();
+- Set<String> foundRefNames = new TreeSet<>();
- for (int i = 0; i < 10000; i++) {
- if (!samRecordIterator.hasNext()) {
- break;
@@ -304,11 +402,11 @@ Last-Updated: 2015-01-06
- foundRefNames.add(refName);
- }
-
-- Assert.assertEquals(new TreeSet<String>(references.subList(0, numberFirstReferenceFound)), foundRefNames);
+- Assert.assertEquals(new TreeSet<>(references.subList(0, numberFirstReferenceFound)), foundRefNames);
- }
-
- @DataProvider(name = "testRows")
-- public Object[][] createDataForRowsTest() {
+- private Object[][] createDataForRowsTest() {
- return new Object[][] {
- // primary alignment only
- {"SRR1063272", 0, 99, "SRR1063272.R.1",
@@ -344,8 +442,6 @@ Last-Updated: 2015-01-06
- @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) {
-- if (!SRAAccession.isSupported()) return;
--
- SAMRecord record = getRecordByIndex(acc, recordIndex, false);
-
- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
@@ -355,8 +451,6 @@ Last-Updated: 2015-01-06
- 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) {
-- if (!SRAAccession.isSupported()) return;
--
- SAMRecord record = getRecordByIndex(acc, recordIndex, true);
-
- checkSAMRecord(record, flags, readName, bases, quals, refStart, cigar, refName, mapQ, hasMate, isSecondaryAlignment);
@@ -366,8 +460,6 @@ Last-Updated: 2015-01-06
- 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) {
-- if (!SRAAccession.isSupported()) return;
--
- SAMRecord record = getRecordByIndex(acc, recordIndex, true);
- SAMFileHeader header = record.getHeader();
-
@@ -405,8 +497,6 @@ Last-Updated: 2015-01-06
- 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) {
-- if (!SRAAccession.isSupported()) return;
--
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -448,8 +538,6 @@ Last-Updated: 2015-01-06
- 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) {
-- if (!SRAAccession.isSupported()) return;
--
- SamReader reader = SamReaderFactory.make().validationStringency(ValidationStringency.SILENT).open(
- SamInputResource.of(new SRAAccession(acc))
- );
@@ -542,153 +630,4 @@ Last-Updated: 2015-01-06
- }
- }
-
-- private void checkAlignedUnalignedCountsByIterator(SAMRecordIterator samRecordIterator,
-- int numberAlignments, int numberUnalignments) {
-- int countAlignments = 0, countUnalignments = 0;
-- while (true) {
-- boolean hasRecord = samRecordIterator.hasNext();
-- SAMRecord record = null;
-- try {
-- record = samRecordIterator.next();
-- Assert.assertTrue(hasRecord); // exception is not thrown if we came to this point
-- } catch (NoSuchElementException e) {
-- Assert.assertFalse(hasRecord);
-- }
--
-- Assert.assertEquals(hasRecord, record != null);
--
-- if (record == null) {
-- break;
-- }
--
-- if (record.getReadUnmappedFlag()) {
-- countUnalignments++;
-- } else {
-- countAlignments++;
-- }
-- }
--
-- Assert.assertEquals(numberAlignments, countAlignments);
-- Assert.assertEquals(numberUnalignments, countUnalignments);
-- }
- }
---- a/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
-+++ b/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
-@@ -52,99 +52,4 @@
- private static final int LAST_BIN_LEVEL = GenomicIndexUtil.LEVEL_STARTS.length - 1;
- private static final int SRA_BIN_OFFSET = GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL];
-
-- @Test
-- public void testLevelSize() {
-- if (!SRAAccession.isSupported()) return;
--
-- SRAIndex index = getIndex(DEFAULT_ACCESSION);
-- Assert.assertEquals(index.getLevelSize(0), GenomicIndexUtil.LEVEL_STARTS[1] - GenomicIndexUtil.LEVEL_STARTS[0]);
--
-- Assert.assertEquals(index.getLevelSize(LAST_BIN_LEVEL), GenomicIndexUtil.MAX_BINS - GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL] - 1);
-- }
--
-- @Test
-- public void testLevelForBin() {
-- if (!SRAAccession.isSupported()) return;
--
-- SRAIndex index = getIndex(DEFAULT_ACCESSION);
-- Bin bin = new Bin(0, SRA_BIN_OFFSET);
-- Assert.assertEquals(index.getLevelForBin(bin), LAST_BIN_LEVEL);
-- }
--
-- @DataProvider(name = "testBinLocuses")
-- public Object[][] createDataForBinLocuses() {
-- return new Object[][] {
-- {DEFAULT_ACCESSION, 0, 0, 1, SRAIndex.SRA_BIN_SIZE},
-- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 2}
-- };
-- }
--
-- @Test(dataProvider = "testBinLocuses")
-- public void testBinLocuses(SRAAccession acc, int reference, int binIndex, int firstLocus, int lastLocus) {
-- if (!SRAAccession.isSupported()) return;
--
-- SRAIndex index = getIndex(acc);
-- Bin bin = new Bin(reference, SRA_BIN_OFFSET + binIndex);
--
-- Assert.assertEquals(index.getFirstLocusInBin(bin), firstLocus);
-- Assert.assertEquals(index.getLastLocusInBin(bin), lastLocus);
-- }
--
-- @DataProvider(name = "testBinOverlappings")
-- public Object[][] createDataForBinOverlappings() {
-- return new Object[][] {
-- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE, new HashSet<Integer>(Arrays.asList(0))},
-- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 2, new HashSet<Integer>(Arrays.asList(1))},
-- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE + 1, SRAIndex.SRA_BIN_SIZE * 3, new HashSet<Integer>(Arrays.asList(1, 2))},
-- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE * 2, SRAIndex.SRA_BIN_SIZE * 2 + 1, new HashSet<Integer>(Arrays.asList(1, 2))}
-- };
-- }
--
--
-- @Test(dataProvider = "testBinOverlappings")
-- public void testBinOverlappings(SRAAccession acc, int reference, int firstLocus, int lastLocus, Set<Integer> binNumbers) {
-- if (!SRAAccession.isSupported()) return;
--
-- SRAIndex index = getIndex(acc);
-- Iterator<Bin> binIterator = index.getBinsOverlapping(reference, firstLocus, lastLocus).iterator();
-- Set<Integer> binNumbersFromIndex = new HashSet<Integer>();
-- while (binIterator.hasNext()) {
-- Bin bin = binIterator.next();
-- binNumbersFromIndex.add(bin.getBinNumber() - SRA_BIN_OFFSET);
-- }
--
-- Assert.assertEquals(binNumbers, binNumbersFromIndex);
-- }
--
-- @DataProvider(name = "testSpanOverlappings")
-- public Object[][] createDataForSpanOverlappings() {
-- return new Object[][] {
-- {DEFAULT_ACCESSION, 0, 1, SRAIndex.SRA_BIN_SIZE, new long[] {0, SRAIndex.SRA_CHUNK_SIZE} },
-- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_BIN_SIZE * 2, SRAIndex.SRA_BIN_SIZE * 2 + 1, new long[]{0, SRAIndex.SRA_CHUNK_SIZE} },
-- {DEFAULT_ACCESSION, 0, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE + 1, new long[]{0, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE, SRAIndex.SRA_CHUNK_SIZE * 2} },
-- };
-- }
--
-- @Test(dataProvider = "testSpanOverlappings")
-- public void testSpanOverlappings(SRAAccession acc, int reference, int firstLocus, int lastLocus, long[] spanCoordinates) {
-- if (!SRAAccession.isSupported()) return;
--
-- SRAIndex index = getIndex(acc);
-- BAMFileSpan span = index.getSpanOverlapping(reference, firstLocus, lastLocus);
--
-- long[] coordinatesFromIndex = span.toCoordinateArray();
-- List<Long> coordinatesListFromIndex = new ArrayList<Long>();
-- for (long coordinate : coordinatesFromIndex) {
-- coordinatesListFromIndex.add(coordinate);
-- }
--
-- Assert.assertTrue(Arrays.equals(coordinatesFromIndex, spanCoordinates),
-- "Coordinates mismatch. Expected: " + Arrays.toString(spanCoordinates) +
-- " but was : " + Arrays.toString(coordinatesFromIndex));
-- }
--
-- private SRAIndex getIndex(SRAAccession acc) {
-- SRAFileReader reader = new SRAFileReader(acc);
-- return (SRAIndex) reader.getIndex();
-- }
}
---- a/build.xml
-+++ b/build.xml
-@@ -138,6 +138,15 @@
- </classpath>
- <classfileset dir="${classes.test}">
- <include name="**/Test*.class"/>
-+ <exclude name="**/BAM*.class"/>
-+ <exclude name="**/CRAM*.class"/>
-+ <exclude name="**/SAM*.class"/>
-+ <exclude name="**/Sam*.class"/>
-+ <exclude name="**/Tabix*.class"/>
-+ <exclude name="**/SRA*.class"/>
-+ <exclude name="**/*FTP*.class"/>
-+ <exclude name="**/EnaRef*.class"/>
-+ <exclude name="**/IupacTest*.class"/>
- <include name="**/*Test.class"/>
- </classfileset>
- <jvmarg value="-Xmx2G"/>
--
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