Steffen Möller pushed to branch master at Debian Med / hts-nim-tools
Commits: bf3cc1e9 by Steffen Möller at 2020-11-07T20:31:53+01:00 Ready for peer review - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/import_random.patch - + debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -2,6 +2,4 @@ hts-nim-tools (0.2.0-1) UNRELEASED; urgency=medium * Initial release (Closes: #973650) - Misses brentp's nim modules lapper and kexec - -- Steffen Moeller <[email protected]> Mon, 02 Nov 2020 20:26:54 +0100 ===================================== debian/control ===================================== @@ -1,14 +1,17 @@ Source: hts-nim-tools Section: science Priority: optional -Maintainer: Steffen Moeller <[email protected]> +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Steffen Moeller <[email protected]> Build-Depends: debhelper-compat (= 13), nim, nim-hts-dev, nim-docopt-dev, nim-unicodedb-dev, nim-unicodeplus-dev, - nim-regex-dev + nim-regex-dev, + nim-kexpr-dev, + nim-lapper-dev Standards-Version: 4.5.0 Homepage: https://github.com/brentp/hts-nim-tools Vcs-Browser: https://salsa.debian.org/med-team/hts-nim-tools ===================================== debian/patches/import_random.patch ===================================== @@ -0,0 +1,28 @@ +Description: Reinstante compatibilitz with nim 1.4 +Forward: This is effectively a backport of a change I found in the current + github repository. I asked to tag a new release on + https://github.com/brentp/hts-nim-tools/issues/11 +Author: Steffen Moeller <[email protected]> +Index: hts-nim-tools/src/copy_number_sampler.nim +=================================================================== +--- hts-nim-tools.orig/src/copy_number_sampler.nim ++++ hts-nim-tools/src/copy_number_sampler.nim +@@ -6,6 +6,7 @@ import lapper + import strutils + import tables + import algorithm ++import random + + import ./version + +@@ -84,8 +85,8 @@ proc internal_sampler(ibam:Bam, obam:var + + var po = overlap_p(res[0], record) + +- if res[0].prob < 1 and random(1.0) < res[0].prob: +- if po == 1 or po < 3.0 * random(1.0): ++ if res[0].prob < 1 and rand(1.0) < res[0].prob: ++ if po == 1 or po < 3.0 * rand(1.0): + obam.write(record) + continue + ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +import_random.patch ===================================== debian/rules ===================================== @@ -1,19 +1,19 @@ #!/usr/bin/make -f export DH_VERBOSE = 1 +NIMCACHE=$(CURDIR)/nimcache + %: dh $@ override_dh_auto_build: - # needs kexpr - #nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/bam_filter.nim - # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/hts_nim_tools.nim - # needs lapper - # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/count_reads.nim - # nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/copy_number_sampler.nim - # works! - nim c -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim + nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim + nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr -p:/usr/share/nimble/hts src/bam_filter.nim + nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim + nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim + nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim override_dh_auto_clean: - rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads + rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads src/copy_number_sampler + rm -rf $(NIMCACHE) View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c -- View it on GitLab: https://salsa.debian.org/med-team/hts-nim-tools/-/commit/bf3cc1e96bf3b2449d6ffdd5d55b4003a732585c You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
