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Ported CompareGtcFiles from Picard private repo (#1468)
Made some classes implement AutoCloseable
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src/main/java/picard/arrays/illumina/CompareGtcFiles.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,235 @@ | ||
| package picard.arrays.illumina; | ||
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| import htsjdk.samtools.util.IOUtil; | ||
| import htsjdk.samtools.util.Log; | ||
| import org.broadinstitute.barclay.argparser.Argument; | ||
| import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| import picard.PicardException; | ||
| import picard.cmdline.CommandLineProgram; | ||
| import picard.cmdline.StandardOptionDefinitions; | ||
|
|
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| import java.io.DataInputStream; | ||
| import java.io.File; | ||
| import java.io.FileInputStream; | ||
| import java.lang.reflect.Array; | ||
| import java.lang.reflect.InvocationTargetException; | ||
| import java.lang.reflect.Method; | ||
| import java.math.BigDecimal; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
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| /** | ||
| * A simple tool to compare two Illumina GTC files. | ||
| */ | ||
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| @CommandLineProgramProperties( | ||
| summary = CompareGtcFiles.USAGE_DETAILS, | ||
| oneLineSummary = "Compares two GTC files.", | ||
| programGroup = picard.cmdline.programgroups.GenotypingArraysProgramGroup.class | ||
| ) | ||
| public class CompareGtcFiles extends CommandLineProgram { | ||
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| static final String USAGE_DETAILS = | ||
| "CompareGtcFiles takes two Illumina GTC file and compares their contents to ensure that fields expected to be the same " + | ||
| "are in fact the same. This will exclude any variable field, such as a date. " + | ||
| "The GTC files must be generated on the same chip type. " + | ||
| "<h4>Usage example:</h4>" + | ||
| "<pre>" + | ||
| "java -jar picard.jar CompareGtcFiles \\<br />" + | ||
| " INPUT=input1.gtc \\<br />" + | ||
| " INPUT=input2.gtc \\<br />" + | ||
| " ILLUMINA_NORMALIZATION_MANIFEST=chip_name.bpm.csv \\<br />" + | ||
| "</pre>"; | ||
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| private static final Log log = Log.getInstance(CompareGtcFiles.class); | ||
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| @Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, | ||
| doc = "GTC input files to compare.", | ||
| minElements = 2, | ||
| maxElements = 2) | ||
| public List<File> INPUT; | ||
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| @Argument(shortName = "NORM_MANIFEST", doc = "An Illumina bead pool manifest (a manifest containing the Illumina normalization ids) (bpm.csv)") | ||
| public File ILLUMINA_NORMALIZATION_MANIFEST; | ||
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| private final List<String> errors = new ArrayList<>(); | ||
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| // Ignored methods | ||
| private static final List<String> IGNORED_METHODS = Arrays.asList( | ||
| "getClass", | ||
| "getAutocallDate", | ||
| "getImagingDate", | ||
| // This is the number of TOC entries. It will be different with different versions. | ||
| "getNumberOfEntries", | ||
| // We don't inject these in our gtcs so they will always be blank and so we don't bother comparing. | ||
| "getSampleName", | ||
| "getSamplePlate", | ||
| "getSampleWell"); | ||
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| @Override | ||
| protected int doWork() { | ||
| IOUtil.assertFilesAreReadable(INPUT); | ||
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| InfiniumNormalizationManifest infiniumNormalizationManifest = new InfiniumNormalizationManifest(ILLUMINA_NORMALIZATION_MANIFEST); | ||
| try (InfiniumGTCFile gtcFileOne = new InfiniumGTCFile(new DataInputStream(new FileInputStream(INPUT.get(0))), infiniumNormalizationManifest); | ||
| InfiniumGTCFile gtcFileTwo = new InfiniumGTCFile(new DataInputStream(new FileInputStream(INPUT.get(1))), infiniumNormalizationManifest)) { | ||
| compareGTCFiles(gtcFileOne, gtcFileTwo); | ||
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| // Report errors and exit 1 if any are detected. | ||
| if (!errors.isEmpty()) { | ||
| for (String error : errors) { | ||
| log.error(error); | ||
| } | ||
| return 1; | ||
| } | ||
| } catch (Exception e) { | ||
| throw new PicardException("File error: ", e); | ||
| } | ||
| return 0; | ||
| } | ||
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| private void compareGTCFiles(InfiniumGTCFile gtcFileOne, InfiniumGTCFile gtcFileTwo) throws InvocationTargetException, IllegalAccessException { | ||
| // Compare all fields we expect won't change. | ||
| Method[] methods = gtcFileOne.getClass().getMethods(); | ||
| for (Method method : methods) { | ||
| // Skip ignored methods. | ||
| if (IGNORED_METHODS.contains(method.getName())) { | ||
| continue; | ||
| } | ||
| // Compare all getters | ||
| if (method.getName().startsWith("get") && method.getGenericParameterTypes().length == 0) { | ||
| // If we have a version and they don't match we just want a warning | ||
| // If getter returns an array compare all array values otherwise do an Object compare. | ||
| // If getter returns an array of arrays do deep compare | ||
| if (method.getName().equals("getFileVersion")) { | ||
| compareVersions(method.invoke(gtcFileOne), method.invoke(gtcFileTwo)); | ||
| } else if (method.getReturnType().isArray() && method.getReturnType().getComponentType().isArray()) { | ||
| compareArrayOfArrays(method.invoke(gtcFileOne), method.invoke(gtcFileTwo), | ||
| method.getName()); | ||
| } else if (method.getReturnType().isArray()) { | ||
| compareArrays(method.invoke(gtcFileOne), method.invoke(gtcFileTwo), | ||
| method.getName()); | ||
| } else { | ||
| compare(method.invoke(gtcFileOne), | ||
| method.invoke(gtcFileTwo), method.getName()); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| private void compareVersions(Object versionOne, Object versionTwo) { | ||
| if (!versionOne.equals(versionTwo)) { | ||
| log.warn(String.format("File versions do not match ( %s vs %s )", | ||
| versionOne, versionTwo)); | ||
| } | ||
| } | ||
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| private void compare(Object objectOne, Object objectTwo, String methodName) { | ||
| if (checkNulls(objectOne, objectTwo, methodName)) return; | ||
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| List<String> compareErrors = new ArrayList<>(); | ||
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| if (!objectOne.equals(objectTwo)) { | ||
| compareErrors.add(String.format("%s does not match ( %s vs %s )", | ||
| methodName, objectOne, objectTwo)); | ||
| } | ||
| checkErrors(methodName, compareErrors); | ||
| } | ||
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| private void compareArrays(Object arrayOne, Object arrayTwo, String methodName) { | ||
| if (checkNulls(arrayOne, arrayTwo, methodName)) return; | ||
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| List<String> compareErrors = new ArrayList<>(); | ||
| int differences = arrayDifferences(arrayOne, arrayTwo, methodName, compareErrors); | ||
| if (differences > 0) { | ||
| compareErrors.add(String.format("%s do not match. %d elements of the array differ.", methodName, differences)); | ||
| } | ||
| checkErrors(methodName, compareErrors); | ||
| } | ||
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| private int arrayDifferences(Object arrayOne, Object arrayTwo, String methodName, List<String> compareErrors) { | ||
| int length1 = Array.getLength(arrayOne); | ||
| int length2 = Array.getLength(arrayTwo); | ||
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| int diffCount = 0; | ||
| if (length1 != length2) { | ||
| compareErrors.add(String.format("%s do not match. Arrays of different lengths. ( %d vs %d )", | ||
| methodName, length1, length2)); | ||
| } else { | ||
| for (int i = 0; i < length1; i++) { | ||
| // For floats only compare 3 decimal places | ||
| if (arrayOne.getClass().getComponentType() == float.class) { | ||
| Float float1 = (float) Array.get(arrayOne, i); | ||
| Float float2 = (float) Array.get(arrayTwo, i); | ||
| if (float1.equals(Float.NaN) || float2.equals(Float.NaN)) { | ||
| if (!float1.equals(float2)) diffCount++; | ||
| } else { | ||
| BigDecimal decimal1 = BigDecimal.valueOf(float1).setScale(3, BigDecimal.ROUND_DOWN); | ||
| BigDecimal decimal2 = BigDecimal.valueOf(float2).setScale(3, BigDecimal.ROUND_DOWN); | ||
| if (!decimal1.equals(decimal2)) { | ||
| diffCount++; | ||
| } | ||
| } | ||
| } else if (!Array.get(arrayOne, i).equals(Array.get(arrayTwo, i))) { | ||
| diffCount++; | ||
| } | ||
| } | ||
| } | ||
| return diffCount; | ||
| } | ||
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| private void compareArrayOfArrays(Object arrayOfArraysOne, Object arrayOfArraysTwo, String methodName) { | ||
| List<String> compareErrors = new ArrayList<>(); | ||
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| if (checkNulls(arrayOfArraysOne, arrayOfArraysTwo, methodName)) return; | ||
|
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| int differences = 0; | ||
| int length1 = Array.getLength(arrayOfArraysOne); | ||
| int length2 = Array.getLength(arrayOfArraysTwo); | ||
| if (length1 != length2) { | ||
| compareErrors.add(String.format("%s do not match. Arrays of different lengths. ( %d vs %d )", | ||
| methodName, length1, length2)); | ||
| } else { | ||
| // Iterate over the first array | ||
| for (int i = 0; i < length1; i++) { | ||
| // Iterate over the second array | ||
| Object innerArrayOne = Array.get(arrayOfArraysOne, i); | ||
| Object innerArrayTwo = Array.get(arrayOfArraysTwo, i); | ||
| differences += arrayDifferences(innerArrayOne, innerArrayTwo, methodName, compareErrors); | ||
| } | ||
| if (differences > 0) { | ||
| compareErrors.add(String.format("%s do not match. %d elements of the array differ.", methodName, differences)); | ||
| } | ||
| } | ||
| checkErrors(methodName, compareErrors); | ||
| } | ||
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| private void checkErrors(String methodName, List<String> compareErrors) { | ||
| if (compareErrors.size() > 0) { | ||
| errors.addAll(compareErrors); | ||
| } else { | ||
| log.info(methodName + " IDENTICAL"); | ||
| } | ||
| } | ||
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| private boolean checkNulls(Object objectOne, Object objectTwo, String methodName) { | ||
| if (objectOne == null && objectTwo == null) { | ||
| log.warn(String.format("Field %s is missing from both files. Strange.", methodName)); | ||
| return true; | ||
| } | ||
| // If one is null we assume a version mismatch | ||
| if (objectOne == null || objectTwo == null) { | ||
| log.warn(String.format("Field %s is missing from one of the files. Version mismatch likely", methodName)); | ||
| return true; | ||
| } | ||
| // If they are primitives check for 0 instead of null | ||
| if ((objectOne.equals(0) ^ objectTwo.equals(0)) || (objectOne.equals(0.0f) ^ objectTwo.equals(0.0f))) { | ||
| log.warn(String.format("Field %s is not in both files. Version mismatch likely", methodName)); | ||
| return true; | ||
| } | ||
| return false; | ||
| } | ||
|
|
||
| } |
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