1 package org.broadinstitute.hellbender.tools.spark.bwa; 2 3 import org.broadinstitute.barclay.argparser.Argument; 4 import org.broadinstitute.hellbender.tools.BwaMemIndexImageCreator; 5 6 import java.io.Serializable; 7 8 /** 9 * A collection of the arguments that are used for BWA. 10 */ 11 public class BwaArgumentCollection implements Serializable { 12 private static final long serialVersionUID = 1L; 13 14 public static final String SINGLE_END_ALIGNMENT_FULL_NAME = "single-end-alignment"; 15 public static final String SINGLE_END_ALIGNMENT_SHORT_NAME = "se"; 16 public static final String BWA_MEM_INDEX_IMAGE_FULL_NAME = "bwa-mem-index-image"; 17 public static final String BWA_MEM_INDEX_IMAGE_SHORT_NAME = "image"; 18 19 /** 20 * The BWA-MEM index image file name that you've distributed to each executor. The image file can be generated using 21 * {@link BwaMemIndexImageCreator}. If this argument is not specified, the default behavior is to look for a 22 * file whose name is the FASTA reference file with a <i>.img</i> suffix. 23 */ 24 @Argument(doc = "The BWA-MEM index image file name that you've distributed to each executor", 25 fullName = BWA_MEM_INDEX_IMAGE_FULL_NAME, 26 shortName = BWA_MEM_INDEX_IMAGE_SHORT_NAME, 27 optional = true) 28 public String indexImageFile; 29 30 /** 31 * Run single-end instead of paired-end alignment. 32 */ 33 @Argument(doc = "Run single-end instead of paired-end alignment", 34 fullName = SINGLE_END_ALIGNMENT_FULL_NAME, 35 shortName = SINGLE_END_ALIGNMENT_SHORT_NAME, 36 optional = true) 37 public boolean singleEndAlignment = false; 38 } 39