parser.add_argument('-f','--filter',action='append',help="Filters [Field:Function(lt, le, eq, ne, ge, gt):Value:Type(i (INT), f (FLOAT), s (STRING), b (BOOL))]")
parser.add_argument('-f','--filter',action='append',help="Filters [Field:Function(lt, le, eq, ne, ge, gt):Value]")
["XmapEntryID",'int',int,'A unique line number for the data lines in the XMAP file. Note: For 2-color, the XmapEntryID will begin with the number 2.'],
["QryContigID",'int',int,'Map ID of query map (Contig ID from .cmap file for query)'],
["RefContigID",'int',int,'Map ID of the reference map from the .cmap reference file (the .cmap file may contain multiple reference maps). Note: RefContigIDs must be integers, but they need not be sequential.'],
["QryStartPos",'float',float,'Coordinates of the first aligned label on the query map (Start position of hit on query map)'],
["QryEndPos",'float',float,'Coordinates of the last aligned label on the query map (Stop position of hit on query map)'],
["RefStartPos",'float',float,'Coordinates of the first aligned label on the reference or anchor map'],
["RefEndPos",'float',float,'Coordinates of the last aligned label on the reference or anchor map'],
["Orientation",'string',col_parse_orientation,'The relative orientation of the query map relative to the reference: forward (+) or reverse (-). The convention is that the reference is always positive orientation, so if the query aligns in reverse, it is shown as having negative (-) orientation. Note: For 2-color, the orientation will be the same.'],
["Confidence",'float',float,'Statistical Confidence of result: Negative Log10 of p-value of alignment (without Bonferroni Correction for multiple experiments). Note: For 2-color, the confidence number is the combined confidence of the alignment for both colors.'],
["HitEnum",'string',col_parse_hit_enum,'Pseudo-CIGAR string representing matches (M), insertions (I), or deletions (D) of label sites with respect to the reference or anchor map. Count begins at the leftmost anchor label of that color. Note: When 2 or more anchor sites resolve into a single query site, only the rightmost anchor site is shown matched with the query site and the leftmost associated anchor sites are shown as deletions.'],
["QryLen",'float',float,'Length of query map from _q.cmap.'],
["RefLen",'float',float,'Length of reference map from _r.cmap.'],
["LabelChannel",'int',int,'Color channel of alignment from cmap files. For 1-color data, LabelChannel is 1. For 2-color data: Using -usecolor N, the LabelChannel is N (N = 1 or 2), and there is only one XMAP entry per alignment for the color channel specified by N. Without -usecolor N, LabelChannel is 1 or 2. In this case, there are two XMAP entries (two lines), one for each color channel.'],
["Alignment",'string',col_parse_alignment,'Indices of the aligned site ID pairs. (When the query orientation is reversed ("-"), the query IDs are in descending order.) Count begins at the leftmost anchor label of that color. Note: When two sites in the reference align with the same site in the query, it is an indication that the two sites in the reference failed to resolve. Alignment provides a view of aligned pairs which would normally be ignored by HitEnum (CIGAR string).'],
["_meta_alignment_count_queries",'int',int,'Number of query labels in alignment'],
["_meta_alignment_count_queries_colapses",'int',int,'Number of query label collapses in alignment. A collapse happens when a label matches more than once a reference label'],
["_meta_alignment_count_refs",'int',int,'Number of reference labels in alignment'],
["_meta_alignment_count_refs_colapses",'int',int,'Number of reference label collapses in alignment. A collapse happens when a label matches more than once a query label'],
["_meta_cigar_deletions",'int',int,'Number of deleted labels in CIGAR string'],
["_meta_cigar_insertions",'int',int,'Number of inserted labels in CIGAR string'],
["_meta_cigar_matches",'int',int,'Number of match labels in CIGAR string'],
["_meta_is_max_confidence_for_qry_chrom",'bool',col_parse_bool,'Whether the current RefContigID is the highest confidence match for this QryContigID'],
