/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
/**
* Constants for tags used in our SAM/BAM files
*/
public class ReservedTagConstants {
public static final String READ_GROUP_ID = SAMTag.RG.name(); // Specified in the SAM spec doc
public static final String PROGRAM_GROUP_ID = SAMTag.PG.name(); // Specified in the SAM spec doc
/** Present and set to 1 if a read is a noise read. */
public static final String XN = "XN";
/** Number of nucleotide differences (Specified in the SAM spec doc) */
public static final String NM = SAMTag.NM.name();
/** The sum of the mismatched qualities. */
public static final String XQ = "XQ";
/**
* The name of an attribute which stores the 1-based index of the start of
* sequence within a read (in original orientation) that should be clipped
* or trimmed before alignment and downstream use.
* The region to be clipped extends from this position to the end of the read.
*/
public static final String XT = "XT";
/** The original sequence before 454 cafie and homopolymer correction */
public static final String XS = "XS";
/** The Four54 edit string of 454 cafie and homopolymer corrections
* <pre>
* editString ::= {base operator position [- position]}* ; // Cafie needs 2 positions
* base ::= A | T | G | C | N ; // N only for undercall
* operator ::= o | u | c ; // o = Overcall, u = Undercall, c = Cafie.
* position is 0 based position of the correction (assuming forward strand) . Cafie positions are to-from.
* For example: XF :Z:Gc4-6Nu11Co15 means a cafie correction moved a G from position 6 to 4,
* an N was inserted for an undercall at position 11, and a C was removed as an overcall at position 15
*/
public static final String XF = "XF";
/** The original pred quality scores before modifications such as 454 cafie and homopolymer correction */
public static final String OQ = SAMTag.OQ.name();
/** The original cigar before indel cleaning, or 454 cafie and homopolymer correction */
public static final String OC = "OC";
}