diff --git a/src/main/java/htsjdk/samtools/SAMTag.java b/src/main/java/htsjdk/samtools/SAMTag.java index 1ea8b88239..a2259c4a81 100644 --- a/src/main/java/htsjdk/samtools/SAMTag.java +++ b/src/main/java/htsjdk/samtools/SAMTag.java @@ -74,6 +74,7 @@ public enum SAMTag { MQ, NH, NM, + OA, OQ, OP, OC, @@ -84,8 +85,8 @@ public enum SAMTag { PQ, PT, PU, - QT, Q2, + QT, QX, R2, RG, diff --git a/src/main/java/htsjdk/samtools/util/SamConstants.java b/src/main/java/htsjdk/samtools/util/SamConstants.java new file mode 100644 index 0000000000..9a6f0456c9 --- /dev/null +++ b/src/main/java/htsjdk/samtools/util/SamConstants.java @@ -0,0 +1,38 @@ +/* + * The MIT License + * + * Copyright (c) 2019 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.util; + +/** + * A set of constants defined in the sam-spec (https://github.com/samtools/hts-specs) that need + * to be referenced in code. + */ + public final class SamConstants { + + //No need to instantiate this class since all the onstants should be static + private SamConstants(){}; + + final static String BARCODE_SEQUENCE_DELIMITER = "-"; + final static String BARCODE_QUALITY_DELIMITER = " "; +}