public String getProgramVersion() { return (String)getAttribute(PROGRAM_VERSION_TAG); }
public String getCommandLine() { return (String)getAttribute(COMMAND_LINE_TAG); }
public String getCommandLine() { return (String)getAttribute(COMMAND_LINE_TAG); }
public String getPreviousProgramGroupId() { return (String)getAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG); }
public String getProgramName() { return (String)getAttribute(PROGRAM_NAME_TAG); }
public String getProgramVersion() { return (String)getAttribute(PROGRAM_VERSION_TAG); }
public String getCommandLine() { return (String)getAttribute(COMMAND_LINE_TAG); }
public String getProgramName() { return (String)getAttribute(PROGRAM_NAME_TAG); }
public String getProgramVersion() { return (String)getAttribute(PROGRAM_VERSION_TAG); }
public String getPreviousProgramGroupId() { return (String)getAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG); }
public String getProgramName() { return (String)getAttribute(PROGRAM_NAME_TAG); }
public String getPreviousProgramGroupId() { return (String)getAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG); }
final SAMProgramRecord record = pair.getHeaderRecord(); final String id = record.getProgramGroupId(); final String ppId = (String) record.getAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG);
final SAMProgramRecord record = pair.getHeaderRecord(); final String id = record.getProgramGroupId(); final String ppId = (String) record.getAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG);
private boolean compareProgramRecord(final SAMProgramRecord programRecord1, final SAMProgramRecord programRecord2) { if (programRecord1 == null && programRecord2 == null) { return true; } if (programRecord1 == null) { reportDifference("null", programRecord2.getProgramGroupId(), "Program Record"); return false; } if (programRecord2 == null) { reportDifference(programRecord1.getProgramGroupId(), "null", "Program Record"); return false; } boolean ret = compareValues(programRecord1.getProgramGroupId(), programRecord2.getProgramGroupId(), "Program Name"); final String[] attributes = {"VN", "CL"}; for (final String attribute : attributes) { ret = compareValues(programRecord1.getAttribute(attribute), programRecord2.getAttribute(attribute), attribute + " Program Record attribute") && ret; } return ret; }
final SAMProgramRecord record = pair.getHeaderRecord(); final String id = record.getProgramGroupId(); final String ppId = (String) record.getAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG);
private boolean compareProgramRecord(final SAMProgramRecord programRecord1, final SAMProgramRecord programRecord2) throws Exception { if (programRecord1 == null && programRecord2 == null) { return true; } if (programRecord1 == null) { reportDifference("null", programRecord2.getProgramGroupId(), "Program Record"); return false; } if (programRecord2 == null) { reportDifference(programRecord1.getProgramGroupId(), "null", "Program Record"); return false; } boolean ret = compareValues(programRecord1.getProgramGroupId(), programRecord2.getProgramGroupId(), "Program Name"); final String[] attributes = {"VN", "CL"}; for (final String attribute : attributes) { ret = compareValues(programRecord1.getAttribute(attribute), programRecord2.getAttribute(attribute), attribute + " Program Record attribute") && ret; } return ret; }
private boolean compareProgramRecord(final SAMProgramRecord programRecord1, final SAMProgramRecord programRecord2) throws Exception { if (programRecord1 == null && programRecord2 == null) { return true; } if (programRecord1 == null) { reportDifference("null", programRecord2.getProgramGroupId(), "Program Record"); return false; } if (programRecord2 == null) { reportDifference(programRecord1.getProgramGroupId(), "null", "Program Record"); return false; } boolean ret = compareValues(programRecord1.getProgramGroupId(), programRecord2.getProgramGroupId(), "Program Name"); final String[] attributes = {"VN", "CL"}; for (final String attribute : attributes) { ret = compareValues(programRecord1.getAttribute(attribute), programRecord2.getAttribute(attribute), attribute + " Program Record attribute") && ret; } return ret; }
private boolean compareProgramRecord(final SAMProgramRecord programRecord1, final SAMProgramRecord programRecord2) { if (programRecord1 == null && programRecord2 == null) { return true; } if (programRecord1 == null) { reportDifference("null", programRecord2.getProgramGroupId(), "Program Record"); return false; } if (programRecord2 == null) { reportDifference(programRecord1.getProgramGroupId(), "null", "Program Record"); return false; } boolean ret = compareValues(programRecord1.getProgramGroupId(), programRecord2.getProgramGroupId(), "Program Name"); final String[] attributes = {"VN", "CL"}; for (final String attribute : attributes) { ret = compareValues(programRecord1.getAttribute(attribute), programRecord2.getAttribute(attribute), attribute + " Program Record attribute") && ret; } return ret; }
Assert.assertEquals(sequenceRecord.getAttribute(intTag), Integer.toString(intValue)); Assert.assertEquals(fileHeader.getReadGroup("L1").getAttribute(floatTag), Float.toString(floatValue)); Assert.assertEquals(fileHeader.getProgramRecord("0").getAttribute(stringTag), stringValue);