adding RDEVAL #52070
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| #!/usr/bin/env bash | ||
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| set -o errexit | ||
| set -o nounset | ||
| set -o xtrace | ||
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| cd "$SRC_DIR" | ||
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| export CXXFLAGS="$CXXFLAGS -O3 -I$PREFIX/include" | ||
| export LDFLAGS="$LDFLAGS -L$PREFIX/lib" | ||
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| make -j"${CPU_COUNT}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" | ||
| install -v -m 0755 build/bin/rdeval "$PREFIX/bin/rdeval" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| diff --git a/Makefile b/Makefile | ||
| index 5823f28..cb3efa1 100644 | ||
| --- a/Makefile | ||
| +++ b/Makefile | ||
| @@ -1,5 +1,5 @@ | ||
| -CXX ?= g++ | ||
| -INCLUDE_DIR = -I./include -I./gfalibs/include | ||
| +CXX ?= ${CXX} | ||
| +INCLUDE_DIR = -I./include -I./gfalibs/include -I${PREFIX}/include | ||
| WARNINGS = -Wall -Wextra | ||
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| CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) | ||
| @@ -12,8 +12,8 @@ SOURCE = src | ||
| INCLUDE = include | ||
| BINDIR := $(BUILD)/.o | ||
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| -LDFLAGS := -pthread | ||
| -LIBS = -lz | ||
| +LDFLAGS := -pthread -L${PREFIX}/lib | ||
| +LIBS := -lz | ||
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| OBJS := main input reads | ||
| BINS := $(addprefix $(BINDIR)/, $(OBJS)) | ||
| @@ -27,7 +27,7 @@ head: $(BINS) gfalibs | $(BUILD) | ||
| all: head validate regenerate | ||
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| $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR) | ||
| - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ | ||
| + $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS) | ||
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| .PHONY: gfalibs | ||
| gfalibs: |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| diff --git a/gfalibs/Makefile b/gfalibs/Makefile | ||
| index de9ab9b..c1766ae 100644 | ||
| --- a/gfalibs/Makefile | ||
| +++ b/gfalibs/Makefile | ||
| @@ -1,5 +1,5 @@ | ||
| -CXX = g++ | ||
| -INCLUDE_DIR = -I./include | ||
| +CXX = $(CXX) | ||
| +INCLUDE_DIR = -I${PREFIX}/include -I./include -I./include/parallel-hashmap | ||
| WARNINGS = -Wall -Wextra | ||
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| CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS) | ||
| @@ -8,7 +8,7 @@ TARGET = gfalibs | ||
| BUILD = build/bin | ||
| SOURCE = src | ||
| INCLUDE = include | ||
| -LDFLAGS := | ||
| +LDFLAGS := -L${PREFIX}/lib | ||
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| SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory) | ||
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| @@ -16,7 +16,7 @@ all: $(SOURCES) | ||
| @ | ||
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| %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h | ||
| - $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ | ||
| + $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@ -lz | ||
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| clean: | ||
| $(RM) *.o | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| {% set name = "rdeval" %} | ||
| {% set version = "0.0.2" %} | ||
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| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
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| source: | ||
| url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip | ||
| sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d | ||
| patches: | ||
| - zlib.patch | ||
| - foo.patch | ||
| - gfalibs.patch | ||
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There was a problem hiding this comment. 💡 Codebase verification Patch files have not been submitted upstream The patches 🔗 Analysis chainVerify patch files and their necessity Three patch files are specified:
Please provide:
Further verify upstream submission of patch files Please run the following script to check if the patches have been submitted upstream via pull requests or commits: 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Description: Check patch contents and related upstream issues
# Check patch contents
for patch in zlib.patch foo.patch gfalibs.patch; do
echo "=== Contents of $patch ==="
if [ -f "recipes/rdeval/$patch" ]; then
cat "recipes/rdeval/$patch"
fi
done
# Check for related upstream issues
gh api repos/vgl-hub/rdeval/issues --jq '.[] | select(.title | contains("patch") or contains("build") or contains("zlib") or contains("gfalibs")) | {title: .title, url: .html_url}'
Length of output: 4190 Script: #!/bin/bash
# Description: Check if patches have been submitted upstream via pull requests or commits
echo "=== Checking Pull Requests for patch submissions ==="
gh pr list --repo vgl-hub/rdeval --json title,url --jq '.[] | select(.title | test("zlib.patch|foo.patch|gfalibs.patch")) | {title: .title, url: .url}'
echo "=== Checking Commit Messages for patch references ==="
gh api repos/vgl-hub/rdeval/commits --paginate --jq '.[] | select(.commit.message | test("zlib.patch|foo.patch|gfalibs.patch")) | {message: .commit.message, url: .html_url}'
Length of output: 561 |
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| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage(name|lower, max_pin="x.x") }} | ||
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| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - make | ||
| host: | ||
| - zlib | ||
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| test: | ||
| commands: | ||
| - rdeval --help | ||
|
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There was a problem hiding this comment. 💡 Codebase verification Binary The test command references 🔗 Analysis chainVerify binary name and enhance test coverage The test command uses
Additionally, consider adding tests with sample data to verify core functionality. 🏁 Scripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# Check source code for binary names
rg -g 'Makefile*' -g '*.cpp' 'rdeval|genodsp'
# Look for example data files that could be used in tests
fd -g '*.fa' -g '*.fasta' -g '*.fastq'
Length of output: 448 Script: #!/bin/bash
# Check source code for binary names
rg -g 'Makefile*' -g '*.cpp' -g '*.h' 'rdeval|genodsp'
# Look for example data files that could be used in tests
fd -e fa -e fasta -e fastq
Length of output: 915 |
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| about: | ||
| home: https://github.com/vgl-hub/{{ name }} | ||
| summary: A general purpose, multithreaded read analysis and manipulation tool. | ||
| license: MIT | ||
| license_family: MIT | ||
| license_file: LICENSE | ||
| dev_url: https://github.com/vgl-hub/{{ name }} | ||
| doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md | ||
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| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| diff --git a/gfalibs/include/output.h b/gfalibs/include/output.h | ||
| index aabbec0..20f0dc1 100644 | ||
| --- a/gfalibs/include/output.h | ||
| +++ b/gfalibs/include/output.h | ||
| @@ -12,7 +12,7 @@ | ||
| #include "gfa-lines.h" | ||
| #include "gfa.h" | ||
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| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "zstream/zstream_common.hpp" | ||
| #include "zstream/ozstream.hpp" | ||
| #include "zstream/ozstream_impl.hpp" | ||
| diff --git a/gfalibs/include/stream-obj.h b/gfalibs/include/stream-obj.h | ||
| index 1faa4df..8e28bf6 100644 | ||
| --- a/gfalibs/include/stream-obj.h | ||
| +++ b/gfalibs/include/stream-obj.h | ||
| @@ -2,7 +2,7 @@ | ||
| #define STREAM_OBJ_H | ||
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| #include <fstream> | ||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
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| class membuf : public std::streambuf { | ||
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| diff --git a/gfalibs/src/stream-obj.cpp b/gfalibs/src/stream-obj.cpp | ||
| index e9694ee..c6eca26 100644 | ||
| --- a/gfalibs/src/stream-obj.cpp | ||
| +++ b/gfalibs/src/stream-obj.cpp | ||
| @@ -5,7 +5,7 @@ | ||
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| #include "bed.h" | ||
| #include "struct.h" | ||
| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "global.h" | ||
| #include "log.h" | ||
| #include "threadpool.h" | ||
| diff --git a/src/reads.cpp b/src/reads.cpp | ||
| index 866f49b..ac714cf 100644 | ||
| --- a/src/reads.cpp | ||
| +++ b/src/reads.cpp | ||
| @@ -14,7 +14,7 @@ | ||
| #include "functions.h" // global functions | ||
| #include "stream-obj.h" | ||
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| -#include "zlib.h" | ||
| +#include <zlib.h> | ||
| #include "zstream/zstream_common.hpp" | ||
| #include "zstream/ozstream.hpp" | ||
| #include "zstream/ozstream_impl.hpp" |
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💡 Codebase verification
parallel-hashmap dependency not declared in meta.yaml.
The addition of
parallel-hashmapinclude path suggests a dependency, but it's not declared inrecipes/rdeval/meta.yaml. Please declareparallel-hashmapas a dependency.🔗 Analysis chain
Verify parallel-hashmap dependency.
The addition of
parallel-hashmapinclude path suggests a dependency. Ensure this dependency is properly declared in the recipe's meta.yaml.Also applies to: 9-9
🏁 Scripts executed
The following scripts were executed for the analysis:
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Length of output: 2649