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.)
samtools · Jan 7, 2025 · a6a4504 · a6a4504
1 parent 6d166e7
commit a6a4504
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Showing 8 changed files with 19 additions and 18 deletions.
diff --git 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
+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 → test/SAMtags/LICENSE b/test/SAMtags/LICENSE.md → test/SAMtags/LICENSE
diff --git a/test/bam/LICENSE.md → test/bam/LICENSE b/test/bam/LICENSE.md → test/bam/LICENSE
diff --git a/test/cram/3.0/LICENSE.md → test/cram/3.0/LICENSE b/test/cram/3.0/LICENSE.md → test/cram/3.0/LICENSE
diff --git a/test/cram/3.1/LICENSE.md → test/cram/3.1/LICENSE b/test/cram/3.1/LICENSE.md → test/cram/3.1/LICENSE
diff --git a/test/cram/codecs/LICENSE.md → test/cram/codecs/LICENSE b/test/cram/codecs/LICENSE.md → test/cram/codecs/LICENSE
diff --git a/test/sam/LICENSE.md → test/sam/LICENSE b/test/sam/LICENSE.md → 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 → test/vcf/LICENSE b/test/vcf/LICENSE.md → 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.