Nilesh Patra pushed to branch master at Debian Med / nim-hts
Commits: d7cd93e4 by Nilesh Patra at 2020-11-01T10:44:57+05:30 Add watch file - - - - - f8c670f8 by Nilesh Patra at 2020-11-01T10:47:21+05:30 Repack to remove binary files - - - - - fdcfe021 by Nilesh Patra at 2020-11-01T10:47:32+05:30 New upstream version 0.3.12+ds - - - - - 311cd0f2 by Nilesh Patra at 2020-11-01T10:47:34+05:30 Update upstream source from tag 'upstream/0.3.12+ds' Update to upstream version '0.3.12+ds' with Debian dir 43521ed649d0b5afcbe771e46b17b834ee3057f0 - - - - - fde41403 by Nilesh Patra at 2020-11-01T11:37:34+05:30 Add missing sources for sourceless binaries - - - - - 79c57baf by Nilesh Patra at 2020-11-01T11:37:56+05:30 Regenerate repacked files - - - - - 141a330a by Nilesh Patra at 2020-11-01T11:38:29+05:30 Disable tests for binaries which cannot be generated - - - - - 428af928 by Nilesh Patra at 2020-11-01T11:40:30+05:30 Add upstream/metadata - - - - - 18 changed files: - + debian/README.source - debian/changelog - debian/control - debian/copyright - + debian/missing-sources/HG02002.sam - + debian/patches/disable-test-with-sourceless-file.patch - debian/patches/series - debian/rules - + debian/upstream/metadata - + debian/watch - − tests/HG02002.bam - − tests/HG02002.bam.bai - − tests/other-for-test.bcf.csi - − tests/sa.bam - − tests/sa.bam.bai - − tests/test.bcf.csi - − tests/test.vcf.gz.tbi - − tests/test_files/simple.tsv.gz.csi Changes: ===================================== debian/README.source ===================================== @@ -0,0 +1,19 @@ +Upstream provides binary files without sources for: + +* tests/HG02002.bam.bai +* tests/HG02002.bam + +These have been converted to corresponding text (.sam) files with command: +* samtools view -h -o <out>.sam <in>.bam + +And the corresponding *.sam files are added to: debian/missing-sources + +They can be generated back with the following commands: +* cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam +* samtools index tests/HG02002.bam tests/HG02002.bam.bai + + +These commands are also being run in debian/rules since these binaries are needed for autopkgtests. + + -- Nilesh Patra <[email protected]> Sun, 01 Nov 2020 11:14:35 +0530 + ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -nim-hts (0.3.12-1) UNRELEASED; urgency=medium +nim-hts (0.3.12+ds-1) UNRELEASED; urgency=medium * Initial release (Closes: #973510) ===================================== debian/control ===================================== @@ -6,7 +6,10 @@ Uploaders: Steffen Moeller <[email protected]>, Debian Nim Team <[email protected]> Build-Depends: debhelper-compat (= 13), nim, - libhts-dev + libhts-dev, + samtools, + tabix, + bcftools Standards-Version: 4.5.0 Homepage: https://github.com/brentp/hts-nim Vcs-Browser: https://salsa.debian.org/med-team/nim-hts ===================================== debian/copyright ===================================== @@ -1,6 +1,10 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: nim-hts Source: https://github.com/brentp/hts-nim +Files-Excluded: tests/*.bam* + tests/*.tbi + tests/test_files/*.csi + tests/*.csi Files: * Copyright: 2017-2020 Brent Pedersen ===================================== debian/missing-sources/HG02002.sam ===================================== The diff for this file was not included because it is too large. ===================================== debian/patches/disable-test-with-sourceless-file.patch ===================================== @@ -0,0 +1,39 @@ +Description: Two binaries: +1. tests/other-for-test.bcf.csi - has undergone a lossy transformation and source can't be recovered +2. tests/test_files/simple.tsv.gz.csi - cannot be indexed properly from the existing tsv +Hence disabled tests involving these +Author: Nilesh Patra <[email protected]> +Forwarded: not-needed +Last-Update: 2020-11-01 +--- a/tests/vcftest.nim ++++ b/tests/vcftest.nim +@@ -246,10 +246,10 @@ + check variant.info.set("myflag", val) == Status.OK + check "myflag" notin variant.tostring() + +- test "load index": ++ #[test "load index": + var vcf:VCF + check open(vcf, "tests/test.bcf") +- vcf.load_index("tests/other-for-test.bcf.csi") ++ vcf.load_index("tests/other-for-test.bcf.csi")]# + + test "remove info from header": + var vcf:VCF +--- a/tests/bgzftest.nim ++++ b/tests/bgzftest.nim +@@ -90,7 +90,7 @@ + check reg == "aaa\t4\t10" + check found == 1 + +- test "bgzi-query from VCF rows": ++ #[test "bgzi-query from VCF rows": + ## There was a discrepancy between rec.POS (int32) and BGZI.query (int64) + var db:BGZI + check db.open("tests/test_files/simple.tsv.gz") +@@ -102,4 +102,4 @@ + for row in db.query($rec.CHROM, rec.POS - 1, rec.POS): + rows.add row + check rows.len == 1 +- check rows[0] == "1\t10492\tC\tT" ++ check rows[0] == "1\t10492\tC\tT"]# ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ dontDoNestedTests.patch +disable-test-with-sourceless-file.patch ===================================== debian/rules ===================================== @@ -6,6 +6,13 @@ DEB_BUILD_OPTIONS += nodoc dh $@ override_dh_auto_test: + # Regenerate repacked files + cat tests/sa.sam | samtools view -Sb - > tests/sa.bam + samtools index tests/sa.bam tests/sa.bam.bai + cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam + samtools index tests/HG02002.bam tests/HG02002.bam.bai + tabix tests/test.vcf.gz + bcftools index tests/test.bcf #nim c -p=/usr/share/nimble/unicodedb/ -p=/usr/share/nimble/unicodeplus/ -p=/usr/share/nimble/regex/ test/test.nim #nim c tests/run.nim #./tests/run ===================================== debian/upstream/metadata ===================================== @@ -0,0 +1,7 @@ +--- +Archive: GitHub +Bug-Database: https://github.com/brentp/hts-nim/issues +Bug-Submit: https://github.com/brentp/hts-nim/issues/new +Changelog: https://github.com/brentp/hts-nim/tags +Repository: https://github.com/brentp/hts-nim.git +Repository-Browse: https://github.com/brentp/hts-nim ===================================== debian/watch ===================================== @@ -0,0 +1,4 @@ +version=4 + +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \ +https://github.com/brentp/hts-nim/releases .*/archive/v?@ANY_VERSION@\.tar\.gz ===================================== tests/HG02002.bam deleted ===================================== Binary files a/tests/HG02002.bam and /dev/null differ ===================================== tests/HG02002.bam.bai deleted ===================================== Binary files a/tests/HG02002.bam.bai and /dev/null differ ===================================== tests/other-for-test.bcf.csi deleted ===================================== Binary files a/tests/other-for-test.bcf.csi and /dev/null differ ===================================== tests/sa.bam deleted ===================================== Binary files a/tests/sa.bam and /dev/null differ ===================================== tests/sa.bam.bai deleted ===================================== Binary files a/tests/sa.bam.bai and /dev/null differ ===================================== tests/test.bcf.csi deleted ===================================== Binary files a/tests/test.bcf.csi and /dev/null differ ===================================== tests/test.vcf.gz.tbi deleted ===================================== Binary files a/tests/test.vcf.gz.tbi and /dev/null differ ===================================== tests/test_files/simple.tsv.gz.csi deleted ===================================== Binary files a/tests/test_files/simple.tsv.gz.csi and /dev/null differ View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666 -- View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666 You're receiving this email because of your account on salsa.debian.org.
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