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feat: add wrapping counting filter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| package picard.filter; | ||
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| import htsjdk.samtools.SAMRecord; | ||
| import htsjdk.samtools.filter.SamRecordFilter; | ||
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| /** | ||
| * A CountingFilter that wraps any SamRecordFilter and provides a count of the reads and bases filtered | ||
| */ | ||
| public class CountingFilterWrapper extends CountingFilter { | ||
| private final SamRecordFilter wrappedFilter; | ||
| public CountingFilterWrapper(SamRecordFilter wrappedFilter) { | ||
| this.wrappedFilter = wrappedFilter; | ||
| } | ||
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| @Override | ||
| public boolean reallyFilterOut(SAMRecord record) { | ||
| return wrappedFilter.filterOut(record); | ||
| } | ||
| } |
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50
src/test/java/picard/analysis/CollectUmiPrevalenceMetricsTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| package picard.analysis; | ||
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| import htsjdk.samtools.metrics.MetricsFile; | ||
| import htsjdk.samtools.util.Histogram; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.Test; | ||
| import picard.cmdline.CommandLineProgramTest; | ||
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| import java.io.File; | ||
| import java.io.FileReader; | ||
| import java.io.IOException; | ||
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| import static org.testng.Assert.*; | ||
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| public class CollectUmiPrevalenceMetricsTest extends CommandLineProgramTest { | ||
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| @Override | ||
| public String getCommandLineProgramName() { return CollectUmiPrevalenceMetrics.class.getSimpleName();} | ||
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| @Test | ||
| public void integrationTest() throws IOException { | ||
| final File TEST_DIR = new File("testdata/picard/independent_replicates/"); | ||
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| final File samFile = new File(TEST_DIR, "twopairsWithManyUmis.sam"); | ||
| final File metricsFile = File.createTempFile("test", ".umi_hist"); | ||
| metricsFile.deleteOnExit(); | ||
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| final String[] args = new String[]{ | ||
| "INPUT=" + samFile.getAbsolutePath(), | ||
| "OUTPUT=" + metricsFile.getAbsolutePath(), | ||
| "MINIMUM_MQ=20" | ||
| }; | ||
| Assert.assertEquals(runPicardCommandLine(args), 0); | ||
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| final MetricsFile<?, Integer> output = new MetricsFile<>(); | ||
| output.read(new FileReader(metricsFile)); | ||
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| final Histogram<Integer> hist = output.getHistogram(); | ||
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| assertNull(hist.get(1)); | ||
| assertEquals(hist.get(2).getValue(),4); | ||
| assertEquals(hist.get(3).getValue(),1); | ||
| assertEquals(hist.get(4).getValue(),1); | ||
| assertNull(hist.get(5)); | ||
| assertNull(hist.get(6)); | ||
| assertEquals(hist.getCount(),6); // sets | ||
| assertEquals(hist.getSum(),15); // unique barcodes (in sets) | ||
| } | ||
| } |
30 changes: 30 additions & 0 deletions
30
testdata/picard/independent_replicates/twopairsWithManyUmis.sam
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| @HD VN:1.0 SO:coordinate | ||
| @SQ SN:chr1 LN:501 | ||
| @SQ SN:chr2 LN:501 | ||
| @SQ SN:chr3 LN:501 | ||
| @SQ SN:chr4 LN:101 | ||
| @SQ SN:chr5 LN:101 | ||
| @SQ SN:chr6 LN:101 | ||
| @SQ SN:chr7 LN:404 | ||
| @SQ SN:chr8 LN:202 | ||
| @RG ID:1AAXX.3 SM:test LB:mylib.yossi PL:ILLUMINA | ||
| @PG ID:bwa PN:bwa VN:3 CL:bwa aln | ||
| @CO manually created file. second pair is a copy of the first pair except that it's marked as a duplicate, and the 10th base of the | ||
| @CO first read is modified C->t (lower case for easy view). this corresponds to position 11 | ||
| @CO 123456789 123456789 123456789 123456789 123456789 1234567890 | ||
| 1AAXX.3.1.1 83 chr1 1 255 101M = 302 0201 CAACAGAAGCCGGTATCTGaGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1AAXX.3.1.2 83 chr1 1 255 101M = 302 0201 CAACAGAAGCtGGNATCTGaGcTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1AAXX.3.1.1 163 chr1 302 255 101M = 1 -201 NCGCGGCATCcCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1AAXX.3.1.2 163 chr1 302 255 101M = 1 -201 NCGCGGCATCcCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1AAXX.3.2.1 99 chr2 1 255 101M = 302 0201 CAACAGAAGCCGGTATCTGaGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1AAXX.3.2.2 163 chr2 1 255 101M = 302 0201 CAACAGAAGCtGGNATCTGaGcTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1AAXX.3.2.1 147 chr2 302 255 101M = 1 -201 NCGCGGCATCcCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1AAXX.3.2.2 83 chr2 302 255 101M = 1 -201 NCGCGGCATCcCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1ACXX.3.3.1 83 chr3 2 255 101M = 303 +201 AACAGAAGCCGGTATCTGaGTTTGTGTTTCgGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAANN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1ACXX.3.3.2 83 chr3 2 255 101M = 303 +201 AACAGAAGCtGGNATCTGaGcTTGTGTTTCgGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAANN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1ACXX.3.4.1 83 chr3 2 255 101M = 303 +201 AACAGAAGCCGGTATCTGaGTTTGTGTTTCgGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAANN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1ACXX.3.4.2 83 chr3 2 255 101M = 303 +201 AACAGAAGCtGGNATCTGaGcTTGTGTTTCgGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAANN AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:GG-GG QX:Z:AA AA | ||
| 1ACXX.3.3.1 163 chr3 303 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAAtCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:AA-AA QX:Z:AA AA | ||
| 1ACXX.3.3.2 163 chr3 303 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAAtCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:CC-CC QX:Z:AA AA | ||
| 1ACXX.3.4.1 163 chr3 303 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAAtCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:TT-TT QX:Z:AA AA | ||
| 1ACXX.3.4.2 163 chr3 303 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAAtCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA RG:Z:1AAXX.3 MC:Z:101M RX:Z:GG-GG QX:Z:AA AA |
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