From b97392cec01611e0f5b73a2f2d1dd4f9bf4e37a5 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Thu, 26 Jul 2018 17:11:25 -0400 Subject: [PATCH 1/4] - adding some constants due to recent PR's to the spec. --- src/main/java/htsjdk/samtools/SAMTag.java | 3 ++- src/main/java/htsjdk/samtools/util/SamConstants.java | 11 +++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 src/main/java/htsjdk/samtools/util/SamConstants.java 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..3338c196b6 --- /dev/null +++ b/src/main/java/htsjdk/samtools/util/SamConstants.java @@ -0,0 +1,11 @@ +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 class SamConstants { + + final static String BARCODE_SEQUENCE_DELIMITER = "-"; + final static String BARCODE_QUALITY_DELIMITER = "~"; +} From 192542a47412a8f34ce613d1ee6b255eab8c5124 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Fri, 21 Dec 2018 14:38:55 -0500 Subject: [PATCH 2/4] - oops --- src/main/java/htsjdk/samtools/util/SamConstants.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/htsjdk/samtools/util/SamConstants.java b/src/main/java/htsjdk/samtools/util/SamConstants.java index 3338c196b6..c4487a5af6 100644 --- a/src/main/java/htsjdk/samtools/util/SamConstants.java +++ b/src/main/java/htsjdk/samtools/util/SamConstants.java @@ -7,5 +7,5 @@ public class SamConstants { final static String BARCODE_SEQUENCE_DELIMITER = "-"; - final static String BARCODE_QUALITY_DELIMITER = "~"; + final static String BARCODE_QUALITY_DELIMITER = " "; } From 421c421b82c9b2ba0e6c8c3412d8cb8b0f268550 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Thu, 24 Jan 2019 12:15:17 -0500 Subject: [PATCH 3/4] Update src/main/java/htsjdk/samtools/util/SamConstants.java Co-Authored-By: yfarjoun --- src/main/java/htsjdk/samtools/util/SamConstants.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/htsjdk/samtools/util/SamConstants.java b/src/main/java/htsjdk/samtools/util/SamConstants.java index c4487a5af6..b531849edb 100644 --- a/src/main/java/htsjdk/samtools/util/SamConstants.java +++ b/src/main/java/htsjdk/samtools/util/SamConstants.java @@ -4,7 +4,7 @@ * A set of constants defined in the sam-spec (https://github.com/samtools/hts-specs) that need * to be referenced in code. */ -public class SamConstants { + public final class SamConstants { final static String BARCODE_SEQUENCE_DELIMITER = "-"; final static String BARCODE_QUALITY_DELIMITER = " "; From ed934753b2de663031ace456f2deba7a6481a7df Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Thu, 24 Jan 2019 12:20:42 -0500 Subject: [PATCH 4/4] - add licence - make constructor private --- .../htsjdk/samtools/util/SamConstants.java | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/main/java/htsjdk/samtools/util/SamConstants.java b/src/main/java/htsjdk/samtools/util/SamConstants.java index b531849edb..9a6f0456c9 100644 --- a/src/main/java/htsjdk/samtools/util/SamConstants.java +++ b/src/main/java/htsjdk/samtools/util/SamConstants.java @@ -1,3 +1,27 @@ +/* + * 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; /** @@ -6,6 +30,9 @@ */ 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 = " "; }