#439 extended documentation of GRIDSS SAM tag

src/main/java/au/edu/wehi/idsv/sam/SamTags.java

@@ -1,17 +1,102 @@
 package au.edu.wehi.idsv.sam;
 
 public class SamTags {
+	/**
+	 * Flag indicating whether the "read" is a GRIDSS breakend assembly
+	 */
 	public static final String IS_ASSEMBLY = "aa";
+	/**
+	 * Indicates whether this assembly was generated from forward-supporting
+	 * or backwards-supporting evidence.
+	 *
+	 * "b" indicates a backwards assembly with the anchoring bases expected at the end
+	 *
+	 * "f" indicates a forward assembly with the anchoring bases expected at the start
+	 *
+	 */
 	public static final String ASSEMBLY_DIRECTION = "ad";
+	/**
+	 * Flag indicating whether the breakend assembly was unanchored.
+	 * That is, the assembly did not contain any supporting
+	 * soft clipped/split reads and the read pairs were unable to be
+	 * assembled all the way back to reference-supporting bases.
+	 */
 	public static final String UNANCHORED = "ua";
+	/**
+	 * Strand bias of alignment of supporting soft-clip/split reads.
+	 *
+	 * Bias is between 0 and 1.
+	 * 1 indicates that all assembled SC/SR reads were aligned to the positive strand.
+	 * 0 indicates that all assembled SC/SR reads were aligned to the negative strand.
+	 * The default value is 0.5
+	 */
 	public static final String ASSEMBLY_STRAND_BIAS = "sb";
+	/**
+	 * 0-based start offset of supporting evidence.
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_OFFSET_START = "os";
+	/**
+	 * 0-based assembly contig start offset of supporting evidence.
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_OFFSET_END = "oe";
+	/**
+	 * Type of assembly evidence support. See {@link au.edu.wehi.idsv.AssemblyEvidenceSupport.SupportType}
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_TYPE = "et";
+	/**
+	 * Category of assembly evidence support.
+	 * Categories correspond to the 0-based ordinal of the VCF FORMAT support breakdown.
+	 * By default there is a 1-1 correspondence between input bams and categories.
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_CATEGORY = "ec";
+	/**
+	 * QUAL score of assembly evidence support.
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_QUAL = "eq";
+	/**
+	 * EvidenceID of assembly evidence support. See {@link au.edu.wehi.idsv.EvidenceIdentifierGenerator}
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_EVIDENCEID = "ez";
+	/**
+	 * Fragment identifier of supporting evidence.
+	 * By default, the fragment identifier is just the read name.
+	 *
+	 * This field is used by {@link au.edu.wehi.idsv.vcf.VcfInfoAttributes#BREAKPOINT_VARIANT_FRAGMENTSVARIANT_FRAGMENTS }
+	 * and {@link au.edu.wehi.idsv.vcf.VcfInfoAttributes#BREAKEND_VARIANT_FRAGMENTS } to correctly count the number
+	 * of distinct fragments supporting a variant.
+	 *
+	 * One value per assembled supporting evidence (SC/SR/OEA/DP)
+	 * These fields are used to pro-rata assembly support.
+	 * This prevents a somatic SV adjacent to a germline indel adjacent being flagged as germline.
+	 */
 	public static final String ASSEMBLY_EVIDENCE_FRAGMENTID = "ef";
+	/**
+	 * Maximum length of reads contributing to assembly.
+	 */
 	public static final String ASSEMBLY_MAX_READ_LENGTH = "dl";
 	/***
 	 * Pair of integers indicating how many bases at the start/end of the contig were truncated