Antoni Villalonga pushed to branch master at Debian Med / vt
Commits: 5ec43202 by Antoni Villalonga at 2020-06-17T10:31:36+02:00 d/control Add missing dependency on r-base-core - - - - - 950e7d4c by Antoni Villalonga at 2020-06-17T11:04:35+02:00 Makefile use env CXXFLAGS to pass blhc tests - - - - - 5fbf3eeb by Antoni Villalonga at 2020-06-18T09:12:38+02:00 Adapted to recent versions of external libs and warn on test errors - - - - - 767b74bc by Antoni Villalonga at 2020-06-18T09:16:23+02:00 Update changelog - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/makefile - debian/patches/series - + debian/patches/test-fail-on-error Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +vt (0.57721-2) UNRELEASED; urgency=medium + + * d/control Add missing dependency on r-base-core + * Makefile use env CXXFLAGS to pass blhc tests + * Adapted to recent versions of external libs and warn on test errors + + -- Antoni Villalonga <[email protected]> Thu, 18 Jun 2020 09:12:40 +0200 + vt (0.57721-1) unstable; urgency=medium * Initial release ===================================== debian/control ===================================== @@ -23,7 +23,9 @@ Rules-Requires-Root: no Package: vt Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, + ${misc:Depends}, + r-base-core, Description: Tool set for short variant discovery in genetic sequence data vt is a variant tool set that discovers short variants from Next Generation Sequencing data. ===================================== debian/patches/makefile ===================================== @@ -1,20 +1,19 @@ Description: Build again external/system libs - Remove local libs + Migration from 1.8 to 1.10 libhts Author: Antoni Villalonga i Noceras <[email protected]> -Last-Update: Wed, 17 Jun 2020 03:31:27 +0200 +Last-Update: Wed, 18 Jun 2020 09:10:04 +0200 --- a/Makefile +++ b/Makefile -@@ -1,6 +1,7 @@ +@@ -1,6 +1,6 @@ OPTFLAG = -O3 -INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS +INCLUDES = -I. -I/usr/share/R/include -+CXXFLAGS += $$(CXXFLAGS) -+CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 ++CXXFLAGS += -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 CXX = g++ SOURCESONLY = -@@ -139,52 +140,26 @@ +@@ -139,52 +139,26 @@ TARGET = vt TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY) TOOLOBJ = $(TOOLSRC:.cpp=.o) @@ -86,7 +85,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200 if (i==buffer.end()) { - int32_t cutoff_pos1 = std::max(bcf_get_pos1(buffer.front())-window,1); -+ int32_t cutoff_pos1 = std::max((int)bcf_get_pos1(buffer.front())-window,1); ++ int32_t cutoff_pos1 = std::max((int32_t)bcf_get_pos1(buffer.front())-window,1); if (bcf_get_pos1(v)<cutoff_pos1) { fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", @@ -95,7 +94,7 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200 if (buffer.size()>1) { - int32_t cutoff_pos1 = std::max(bcf_get_pos1(buffer.front())-window,1); -+ int32_t cutoff_pos1 = std::max((int)bcf_get_pos1(buffer.front())-window,1); ++ int32_t cutoff_pos1 = std::max((int32_t)bcf_get_pos1(buffer.front())-window,1); while (buffer.size()>1) { @@ -233,3 +232,25 @@ Last-Update: Wed, 17 Jun 2020 03:31:27 +0200 #include "candidate_region_extractor.h" #include "candidate_motif_picker.h" #include "flank_detector.h" +--- a/hts_utils.h ++++ b/hts_utils.h +@@ -40,9 +40,11 @@ + *FAI UTILS + **********/ + typedef struct { ++ int id; // faidx_t->name[id] is for this struct. + int32_t line_len, line_blen; + int64_t len; + uint64_t offset; ++ uint64_t qual_offset; + } faidx1_t; + + KHASH_MAP_INIT_STR(s, faidx1_t) +@@ -52,6 +54,7 @@ + int n, m; + char **name; + khash_t(s) *hash; ++ enum fai_format_options format; + }; + + /** ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ makefile fix-spelling +test-fail-on-error ===================================== debian/patches/test-fail-on-error ===================================== @@ -0,0 +1,8 @@ +--- a/test/test.sh ++++ b/test/test.sh +@@ -235,3 +235,5 @@ + echo -n ${PASSED_TESTS} + echo -n " / " + echo ${NO_TESTS} ++ ++[ ${PASSED_TESTS} -eq ${NO_TESTS} ] View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da -- View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/489a79eb6389c9abc44aa26e829dfc53b5102392...767b74bceabe6672ed178e999721e5c1186a63da You're receiving this email because of your account on salsa.debian.org.
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