Hello team ,I've updated delly[1] to the latest upstream version (1.3.1) . Also I've added in autopkgtests,fixed blhc and made the builds reproducible. The CI shows an autopkgtest failure as of now[2] which I think is related to an issue with the CI infra. The autopkgtests works fine when run locally :
autopkgtest [16:17:13]: test run-unit-test: [----------------------- Running Tests Test 1 [2022-Aug-11 10:47:13] delly call -o sr.bcf -g ref.fa sr.bam [2022-Aug-11 10:47:13] Paired-end and split-read scanning [2022-Aug-11 10:47:13] Split-read clustering [2022-Aug-11 10:47:13] Paired-end clustering [2022-Aug-11 10:47:13] Split-read assembly [2022-Aug-11 10:47:13] Generate REF and ALT probes [2022-Aug-11 10:47:13] SV annotation [2022-Aug-11 10:47:14] Genotyping [2022-Aug-11 10:47:14] Sample statistics Sample:sr,ReadSize=150,Median=501,MAD=33,UniqueDiscordantPairs=9 [2022-Aug-11 10:47:14] Done. Test 2 [2022-Aug-11 10:47:14] delly lr -g ref.fa lr.bam -o lr.vcf [2022-Aug-11 10:47:14] Split-read scanning [2022-Aug-11 10:47:14] Split-read assembly [2022-Aug-11 10:47:14] Generate REF and ALT probes [2022-Aug-11 10:47:14] Select reads [2022-Aug-11 10:47:14] Align to REF and ALT [2022-Aug-11 10:47:14] Genotyping [2022-Aug-11 10:47:14] Done. Test 3 [2022-Aug-11 10:47:14] delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf [2022-Aug-11 10:47:14] Scanning Windows [2022-Aug-11 10:47:14] Estimate GC bias [2022-Aug-11 10:47:14] Count fragments [2022-Aug-11 10:47:14] Genotyping [2022-Aug-11 10:47:14] Done. PASS autopkgtest [16:17:14]: test run-unit-test: -----------------------]autopkgtest [16:17:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test PASS autopkgtest [16:17:15]: @@@@@@@@@@@@@@@@@@@@ summary run-unit-test PASS Requesting someone to review and sponsor my changes :) [1] - https://salsa.debian.org/med-team/delly [2] - https://salsa.debian.org/med-team/delly/-/jobs/3093817 Thanks -- ╭────────────────────────────────────────────────────╮ │ Mohammed Bilal │ │ 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F │ ╰────────────────────────────────────────────────────╯
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