public void setProgramName(final String name) { setAttribute(PROGRAM_NAME_TAG, name); }
public void setProgramName(final String name) { setAttribute(PROGRAM_NAME_TAG, name); }
public void setCommandLine(final String commandLine) { setAttribute(COMMAND_LINE_TAG, commandLine); }
public void setPreviousProgramGroupId(final String id) { setAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG, id); }
public void setProgramVersion(final String version) { setAttribute(PROGRAM_VERSION_TAG, version); }
public void setProgramVersion(final String version) { setAttribute(PROGRAM_VERSION_TAG, version); }
public void setCommandLine(final String commandLine) { setAttribute(COMMAND_LINE_TAG, commandLine); }
public void setProgramVersion(final String version) { setAttribute(PROGRAM_VERSION_TAG, version); }
public void setPreviousProgramGroupId(final String id) { setAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG, id); }
public void setPreviousProgramGroupId(final String id) { setAttribute(PREVIOUS_PROGRAM_GROUP_ID_TAG, id); }
public void setProgramName(final String name) { setAttribute(PROGRAM_NAME_TAG, name); }
public void setCommandLine(final String commandLine) { setAttribute(COMMAND_LINE_TAG, commandLine); }
public SAMProgramRecord(final String id, SAMProgramRecord srcProgramRecord) { mProgramGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
public SAMProgramRecord(final String id, SAMProgramRecord srcProgramRecord) { mProgramGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
public SAMProgramRecord(final String id, SAMProgramRecord srcProgramRecord) { mProgramGroupId = id; for (final Map.Entry<String, String> entry : srcProgramRecord.getAttributes()) { setAttribute(entry.getKey(), entry.getValue()); } }
translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId); } else if (needToTranslateId) { translatedRecord = new SAMProgramRecord(translatedId, record); } else if (needToTranslatePpId) { translatedRecord = new SAMProgramRecord(id, record); translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId);
translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId); } else if (needToTranslateId) { translatedRecord = new SAMProgramRecord(translatedId, record); } else if (needToTranslatePpId) { translatedRecord = new SAMProgramRecord(id, record); translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId);
translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId); } else if(needToTranslateId) { translatedRecord = new SAMProgramRecord(translatedId, record); } else if(needToTranslatePpId) { translatedRecord = new SAMProgramRecord(id, record); translatedRecord.setAttribute(SAMProgramRecord.PREVIOUS_PROGRAM_GROUP_ID_TAG, translatedPpId);
public static SAMFileHeader buildSAMFileHeader(AlignmentHeader alignmentHeader){ SAMFileHeader samFileHeader = new SAMFileHeader(); for(Map.Entry<String, String> entry : alignmentHeader.getAttributes().entrySet()) { samFileHeader.setAttribute(entry.getKey(), entry.getValue()); } for(AlignmentHeader.SequenceRecord sq : alignmentHeader.getSequenceDiccionary()){ SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(sq.getSequenceName(), sq.getSequenceLength()); for(Map.Entry<String, String> entry : sq.getAttributes().entrySet()) samSequenceRecord.setAttribute(entry.getKey(), entry.getValue()); samFileHeader.addSequence(samSequenceRecord); } for(AlignmentHeader.ReadGroup rg : alignmentHeader.getReadGroups()){ SAMReadGroupRecord samReadGroupRecord = new SAMReadGroupRecord(rg.getId()); for(Map.Entry<String, String> entry : rg.getAttributes().entrySet()){ samReadGroupRecord.setAttribute(entry.getKey(), entry.getValue()); } samFileHeader.addReadGroup(samReadGroupRecord); } for(AlignmentHeader.ProgramRecord pg : alignmentHeader.getProgramRecords()){ SAMProgramRecord samProgramRecord = new SAMProgramRecord(pg.getId()); for(Map.Entry<String, String> entry : pg.getAttributes().entrySet()){ samProgramRecord.setAttribute(entry.getKey(), entry.getValue()); } samFileHeader.addProgramRecord(samProgramRecord); } samFileHeader.setComments(alignmentHeader.getComments()); return samFileHeader; } public static AlignmentHeader buildAlignmentHeader(SAMFileHeader samHeader, String studyName){