public void addPG(SAMFileHeader header, String program, String cmd, String version) { SAMProgramRecord programRecord = header.createProgramRecord(); programRecord.setCommandLine(cmd); programRecord.setProgramName(program); programRecord.setProgramVersion(version); }
@Test public void testGetSAMString() { SAMProgramRecord r = new SAMProgramRecord("SW-eIV"); r.setProgramName("telnet"); r.setProgramVersion("0.17-40"); r.setCommandLine("telnet towel.blinkenlights.nl"); Assert.assertEquals("@PG\tID:SW-eIV\tPN:telnet\tVN:0.17-40\tCL:telnet towel.blinkenlights.nl", r.getSAMString()); } }
programRecord.setProgramVersion(PROGRAM_GROUP_VERSION); programRecord.setCommandLine(PROGRAM_GROUP_COMMAND_LINE); programRecord.setProgramName(PROGRAM_GROUP_NAME); programRecord.setPreviousProgramGroupId(existingId); outputHeader.addProgramRecord(programRecord);
programRecord.setProgramVersion(PROGRAM_GROUP_VERSION); programRecord.setCommandLine(PROGRAM_GROUP_COMMAND_LINE); programRecord.setProgramName(PROGRAM_GROUP_NAME); programRecord.setPreviousProgramGroupId(existingId); outputHeader.addProgramRecord(programRecord);
prod.setProgramVersion(PROGRAM_GROUP_VERSION); prod.setCommandLine(PROGRAM_GROUP_COMMAND_LINE); prod.setProgramName(PROGRAM_GROUP_NAME);
prod.setProgramVersion(PROGRAM_GROUP_VERSION); prod.setCommandLine(PROGRAM_GROUP_COMMAND_LINE); prod.setProgramName(PROGRAM_GROUP_NAME);
final SAMProgramRecord pg = new SAMProgramRecord(String.valueOf(i)); pg.setCommandLine(getCommandLine()); pg.setProgramName(getClass().getSimpleName()); header.addProgramRecord(pg); break;
final SAMProgramRecord pg = new SAMProgramRecord(String.valueOf(i)); pg.setCommandLine(getCommandLine()); pg.setProgramName(getClass().getSimpleName()); header.addProgramRecord(pg); break;
program.setProgramName(PG.getName());
final SAMProgramRecord programRecord = new SAMProgramRecord(pgIdGenerator.getNonCollidingId(PG_PROGRAM_NAME)); programRecord.setProgramName(PG_PROGRAM_NAME); programRecord.setCommandLine(getCommandLine()); programRecord.setProgramVersion(getVersion());
program.setProgramName(PG.getName());
final SAMProgramRecord programRecord = new SAMProgramRecord(pgIdGenerator.getNonCollidingId(PG_PROGRAM_NAME)); programRecord.setProgramName(PG_PROGRAM_NAME); programRecord.setCommandLine(getCommandLine()); programRecord.setProgramVersion(getVersion());