org.broadinstitute.hellbender.tools.spark.pathseq.PSBwaArgumentCollection Maven / Gradle / Ivy
package org.broadinstitute.hellbender.tools.spark.pathseq;
import org.broadinstitute.barclay.argparser.Argument;
import java.io.Serializable;
public final class PSBwaArgumentCollection implements Serializable {
private static final long serialVersionUID = 1L;
public static final String MICROBE_BWA_IMAGE_LONG_NAME = "microbe-bwa-image";
public static final String MICROBE_REF_DICT_LONG_NAME = "microbe-dict";
public static final String MICROBE_MIN_SEED_LENGTH_LONG_NAME = "microbe-min-seed-length";
public static final String MAX_ALT_HITS_LONG_NAME = "max-alternate-hits";
public static final String SCORE_THRESHOLD_LONG_NAME = "bwa-score-threshold";
@Argument(doc = "Microbe reference BWA index image file generated using BwaMemIndexImageCreator. If running on a Spark cluster, this must be distributed to local disk on each node.",
fullName = MICROBE_BWA_IMAGE_LONG_NAME)
public String bwaImage;
@Argument(fullName = MICROBE_REF_DICT_LONG_NAME,
doc = "Use the given sequence dictionary as the microbe sequence dictionary. Must be a .dict file.")
public String microbeDictionary = null;
/**
* This parameter controls the sensitivity of the BWA-MEM aligner. Smaller values result in more alignments at the
* expense of computation time.
*/
@Argument(doc = "Minimum BWA-MEM seed length for the microbe alignment",
fullName = MICROBE_MIN_SEED_LENGTH_LONG_NAME,
minValue = 1,
minRecommendedValue = 11,
optional = true)
public int seedLength = 19;
/**
* The maximum number of alternate alignments for each read, i.e. the alignments appearing in the XA tag.
*/
@Argument(doc = "Maximum number of alternate microbe alignments",
fullName = MAX_ALT_HITS_LONG_NAME,
minValue = 0,
optional = true)
public int maxAlternateHits = 5000;
/**
* This parameter controls the minimum quality of the BWA alignments for the output.
*/
@Argument(doc = "Minimum score threshold for microbe alignments",
fullName = SCORE_THRESHOLD_LONG_NAME,
minValue = 0,
optional = true)
public int scoreThreshold = 30;
public final int bwaThreads = 1;
}