[med-svn] [Git][med-team/hts-nim-tools][master] Ready for peer review

[Steffen Möller]

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 <moeller at debian.org>  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 <moeller at debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>
 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 <moeller at debian.org>
+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
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