Test case for htslib/1620 and htslib/1630 #1938
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daviesrob
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Jun 20, 2023
Add some tests to exercise the --regions / --targets synced reader options. Currently this only includes tests for the chromosomes with [:-] characters in the name, but it could be expanded easily to do others. Test files have been borrowed from pull request samtools/bcftools#1938. Move the synced reader no-index tests from test-bcf-sr.pl to test.pl. The former isn't a good place for them as it gets called 10 times, but the no-index test only needs to run once. It also allows the code running the test to be simplified a bit. Also fix the exit code on test-bcf-sr.pl failure from -1 to 1. Co-authored-by: Petr Danecek <pd3@sanger.ac.uk>
daviesrob
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Jun 20, 2023
Add some tests to exercise the --regions / --targets synced reader options. Currently this only includes tests for the chromosomes with [:-] characters in the name, but it could be expanded easily to do others. Test files have been borrowed from pull request samtools/bcftools#1938. Move the synced reader no-index tests from test-bcf-sr.pl to test.pl. The former isn't a good place for them as it gets called 10 times, but the no-index test only needs to run once. It also allows the code running the test to be simplified a bit. Also fix the exit code on test-bcf-sr.pl failure from -1 to 1. Co-authored-by: Petr Danecek <pd3@sanger.ac.uk>
jkbonfield
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Jun 27, 2023
Add some tests to exercise the --regions / --targets synced reader options. Currently this only includes tests for the chromosomes with [:-] characters in the name, but it could be expanded easily to do others. Test files have been borrowed from pull request samtools/bcftools#1938. Move the synced reader no-index tests from test-bcf-sr.pl to test.pl. The former isn't a good place for them as it gets called 10 times, but the no-index test only needs to run once. It also allows the code running the test to be simplified a bit. Also fix the exit code on test-bcf-sr.pl failure from -1 to 1. Co-authored-by: Petr Danecek <pd3@sanger.ac.uk>
vasudeva8
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Aug 17, 2023
Add some tests to exercise the --regions / --targets synced reader options. Currently this only includes tests for the chromosomes with [:-] characters in the name, but it could be expanded easily to do others. Test files have been borrowed from pull request samtools/bcftools#1938. Move the synced reader no-index tests from test-bcf-sr.pl to test.pl. The former isn't a good place for them as it gets called 10 times, but the no-index test only needs to run once. It also allows the code running the test to be simplified a bit. Also fix the exit code on test-bcf-sr.pl failure from -1 to 1. Co-authored-by: Petr Danecek <pd3@sanger.ac.uk>
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samtools/htslib#1620
samtools/htslib#1630