From a6a4504917a1b02197538f21e1b441c3f3892be4 Mon Sep 17 00:00:00 2001 From: James Bonfield Date: Tue, 6 Aug 2024 16:13:39 +0100 Subject: [PATCH] Renamed LICENSE.md to LICENSE following review (PR #768) Also some minor tweakage of text. In particular examples/vcf/simple.vcf is from VCFv3.1.tex and / or VCFtools, but there is no evidence which came first and they both have differing copyright statements. (All we can do is state what is known and unknown.) --- examples/vcf/simple.vcf | 2 +- test/SAMtags/{LICENSE.md => LICENSE} | 0 test/bam/{LICENSE.md => LICENSE} | 0 test/cram/3.0/{LICENSE.md => LICENSE} | 0 test/cram/3.1/{LICENSE.md => LICENSE} | 0 test/cram/codecs/{LICENSE.md => LICENSE} | 0 test/sam/{LICENSE.md => LICENSE} | 11 +++++------ test/vcf/{LICENSE.md => LICENSE} | 24 +++++++++++++----------- 8 files changed, 19 insertions(+), 18 deletions(-) rename test/SAMtags/{LICENSE.md => LICENSE} (100%) rename test/bam/{LICENSE.md => LICENSE} (100%) rename test/cram/3.0/{LICENSE.md => LICENSE} (100%) rename test/cram/3.1/{LICENSE.md => LICENSE} (100%) rename test/cram/codecs/{LICENSE.md => LICENSE} (100%) rename test/sam/{LICENSE.md => LICENSE} (69%) rename test/vcf/{LICENSE.md => LICENSE} (61%) diff --git a/examples/vcf/simple.vcf b/examples/vcf/simple.vcf index ea0f1f4a9..90104016e 100644 --- a/examples/vcf/simple.vcf +++ b/examples/vcf/simple.vcf @@ -21,4 +21,4 @@ 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 -20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 \ No newline at end of file +20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 diff --git a/test/SAMtags/LICENSE.md b/test/SAMtags/LICENSE similarity index 100% rename from test/SAMtags/LICENSE.md rename to test/SAMtags/LICENSE diff --git a/test/bam/LICENSE.md b/test/bam/LICENSE similarity index 100% rename from test/bam/LICENSE.md rename to test/bam/LICENSE diff --git a/test/cram/3.0/LICENSE.md b/test/cram/3.0/LICENSE similarity index 100% rename from test/cram/3.0/LICENSE.md rename to test/cram/3.0/LICENSE diff --git a/test/cram/3.1/LICENSE.md b/test/cram/3.1/LICENSE similarity index 100% rename from test/cram/3.1/LICENSE.md rename to test/cram/3.1/LICENSE diff --git a/test/cram/codecs/LICENSE.md b/test/cram/codecs/LICENSE similarity index 100% rename from test/cram/codecs/LICENSE.md rename to test/cram/codecs/LICENSE diff --git a/test/sam/LICENSE.md b/test/sam/LICENSE similarity index 69% rename from test/sam/LICENSE.md rename to test/sam/LICENSE index 202ed97c0..4f802d11f 100644 --- a/test/sam/LICENSE.md +++ b/test/sam/LICENSE @@ -3,20 +3,19 @@ submitted the tests. A generic wildcard assignment is for Genome Reseatch Limited as this constitutes the vast bulk of the data, with exceptions listed below. -- `*/*.sam`: +- */*.sam: Copyright (C) 2021 Genome Research Ltd. -- `failed/hdr.SQ14.sam`: +- failed/hdr.SQ14.sam: Copyright (C) 2021 John Marshall -However all files have the same Apache 2.0 license irrespective of -copyright holder. A copy of this license can be found in the GA4GH -Copyright Policy at https://www.ga4gh.org/copyright-policy/ and +All files have the same Apache 2.0 license irrespective of copyright +holder. A copy of this license can be found in the GA4GH Copyright +Policy at https://www.ga4gh.org/copyright-policy/ and https://www.apache.org/licenses/LICENSE-2.0. Note: some files may also contain their own individual copyright and/or license notices, which take precedence over anything listed here. (See compare_sam.pl as an example) - diff --git a/test/vcf/LICENSE.md b/test/vcf/LICENSE similarity index 61% rename from test/vcf/LICENSE.md rename to test/vcf/LICENSE index 7ff691470..c4d592369 100644 --- a/test/vcf/LICENSE.md +++ b/test/vcf/LICENSE @@ -1,7 +1,7 @@ Copyright and licensing for the different files here varies by host institution that submitted the tests. -- `test/vcf/*.vcf`: +- test/vcf/*.vcf: The vast bulk of the test files originated from European Bioinformatics Institute's vcf-validator: @@ -10,7 +10,7 @@ institution that submitted the tests. These are Copyright EBI and the project is Apache 2.0 licensed. See https://www.apache.org/licenses/LICENSE-2.0 -- `test/vcf/4.*/passed/complexfile_passed_000.vcf`: +- test/vcf/4.*/passed/complexfile_passed_000.vcf: Also present in the EBI vcf-validator, however this data looks to be a subset of the 1000 Genomes project so it may be covered by @@ -19,29 +19,31 @@ institution that submitted the tests. See https://www.internationalgenome.org/IGSR_disclaimer and https://www.internationalgenome.org/category/data-access/ -- `examples/vcf/simple.vcf`: +- examples/vcf/simple.vcf: - Part of commit 7aeed5b, but not from the vcf-validator. - Unknown copyright / license, but assumed to be 1000 Genomes. + Copied from the VCF TeX document. The example also appears in VCFtools + (https://sourceforge.net/p/vcftools/code/HEAD/tree/trunk/) which + is LGPLv3, but it is unknown if it was copied to there from the + original spec or vice versa. -- `examples/vcf/sv44.vcf`: +- examples/vcf/sv44.vcf: Copyright Daniel Cameron, 2022. Apache 2.0 license. -- `test/vcf/4.3/failed/failed_body_format_007.vcf`: +- test/vcf/4.3/failed/failed_body_format_007.vcf: Copyright Daniel Cameron, 2023. Apache 2.0 license. -- `test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf`: -- `test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf`: -- `test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf`: +- test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf: +- test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf: +- test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf: Copyright Daniel Cameron, 2024. Apache 2.0 license. -- `test/vcf/4.5/passed/zero_length_LAA.vcf`: +- test/vcf/4.5/passed/zero_length_LAA.vcf: Copyright Daniel Cameron, 2024. Apache 2.0 license.