1 package org.broadinstitute.hellbender.cmdline; 2 3 /** 4 * @author Daniel Gomez-Sanchez (magicDGS) 5 */ 6 public final class ReadFilterArgumentDefinitions { ReadFilterArgumentDefinitions()7 private ReadFilterArgumentDefinitions(){} 8 9 // GATKReadFilterPluginDescriptor arguments 10 11 public static final String READ_FILTER_LONG_NAME = "read-filter"; 12 public static final String DISABLE_READ_FILTER_LONG_NAME = "disable-read-filter"; 13 public static final String DISABLE_TOOL_DEFAULT_READ_FILTERS = "disable-tool-default-read-filters"; 14 public static final String READ_FILTER_SHORT_NAME = "RF"; 15 public static final String DISABLE_READ_FILTER_SHORT_NAME = "DF"; 16 17 // ReadFilter arguments 18 19 public static final String AMBIGUOUS_FILTER_FRACTION_NAME = "ambig-filter-frac"; 20 public static final String AMBIGUOUS_FILTER_BASES_NAME = "ambig-filter-bases"; 21 22 public static final String MAX_FRAGMENT_LENGTH_NAME = "max-fragment-length"; 23 public static final String MIN_FRAGMENT_LENGTH_NAME = "min-fragment-length"; 24 25 public static final String LIBRARY_NAME = "library"; 26 27 public static final String MINIMUM_MAPPING_QUALITY_NAME = "minimum-mapping-quality"; 28 public static final String MAXIMUM_MAPPING_QUALITY_NAME = "maximum-mapping-quality"; 29 30 public static final String FILTER_TOO_SHORT_NAME = "filter-too-short"; 31 public static final String DONT_REQUIRE_SOFT_CLIPS_BOTH_ENDS_NAME = "dont-require-soft-clips-both-ends"; 32 33 public static final String PL_FILTER_NAME_LONG_NAME = "platform-filter-name"; 34 35 public static final String BLACK_LISTED_LANES_LONG_NAME = "black-listed-lanes"; 36 37 public static final String READ_GROUP_BLACK_LIST_LONG_NAME = "read-group-black-list"; 38 39 public static final String KEEP_READ_GROUP_LONG_NAME = "keep-read-group"; 40 41 public static final String MAX_READ_LENGTH_ARG_NAME = "max-read-length"; 42 public static final String MIN_READ_LENGTH_ARG_NAME = "min-read-length"; 43 44 public static final String READ_NAME_LONG_NAME = "read-name"; 45 46 public static final String KEEP_REVERSE_STRAND_ONLY_NAME = "keep-reverse-strand-only"; 47 48 public static final String SAMPLE_NAME = "sample"; 49 50 public static final String KEEP_INTERVAL_NAME = "keep-intervals"; 51 52 public static final String SOFT_CLIPPED_RATIO_THRESHOLD = "soft-clipped-ratio-threshold"; 53 public static final String SOFT_CLIPPED_LEADING_TRAILING_RATIO_THRESHOLD = "soft-clipped-leading-trailing-ratio"; 54 55 public static final String INVERT_SOFT_CLIP_RATIO_FILTER = "invert-soft-clip-ratio-filter"; 56 57 public static final String MATE_TOO_DISTANT_LENGTH = "mate-too-distant-length"; 58 } 59