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Speed up BCF2 and SeekableStream integration tests #1770

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Speed up BCF2 and SeekableStream integration tests #1770

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6 changes: 4 additions & 2 deletions ...est/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,10 @@ private static String generateRandomString(final int length) {
@DataProvider
public Iterator<Object[]> compressedVcfsToTest() throws Exception {
final List<Object[]> data = new ArrayList<>();
final int nSmallRecords = 1000000;
for (int firstRecordLength = 1000; firstRecordLength <= 10000; firstRecordLength+=1000) {
// 100K records is sufficient to exercise multi-block BGZF boundaries and detect the
// GZIPInputStream available() bug. 5 first-record-length variants cover the range.
final int nSmallRecords = 100_000;
for (int firstRecordLength = 1000; firstRecordLength <= 9000; firstRecordLength += 2000) {
data.add(new Object[]{createBgzipVcfsWithVariableSize(firstRecordLength, nSmallRecords), nSmallRecords+1});
}
return data.iterator();
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22 changes: 8 additions & 14 deletions src/test/java/htsjdk/variant/bcf2/BCF2EncoderDecoderUnitTest.java
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Expand Up @@ -120,24 +120,18 @@ public void before() {
primitives.add(new BCF2TypedValue(null, type));
}

// One representative per type plus one null per non-CHAR type. Reducing from 17 to 9
// values cuts the 3-way cartesian product from 4913 to 729 test sequences while still
// covering all type combinations and null handling.
forCombinations.add(new BCF2TypedValue(10, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(100, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(-100, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(-128, BCF2Type.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue( 128, BCF2Type.INT16)); // first value in range
forCombinations.add(new BCF2TypedValue(-100000, BCF2Type.INT32));
forCombinations.add(new BCF2TypedValue(-128, BCF2Type.INT16));
forCombinations.add(new BCF2TypedValue(100000, BCF2Type.INT32));
forCombinations.add(new BCF2TypedValue(0.0, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue(1.23e6, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue(-1.23e6, BCF2Type.FLOAT));
forCombinations.add(new BCF2TypedValue("S", BCF2Type.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));
forCombinations.add(new BCF2TypedValue("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXYZ", BCF2Type.CHAR));

// missing values
for ( BCF2Type type : BCF2Type.values() ) {
forCombinations.add(new BCF2TypedValue(null, type));
}
forCombinations.add(new BCF2TypedValue(null, BCF2Type.INT8));
forCombinations.add(new BCF2TypedValue(null, BCF2Type.INT16));
forCombinations.add(new BCF2TypedValue(null, BCF2Type.INT32));
forCombinations.add(new BCF2TypedValue(null, BCF2Type.FLOAT));
}

// --------------------------------------------------------------------------------
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