Fix CLI/output/packaging issues for Galaxy/Bioconda integration#2
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Adds --version flag, makes input-type detection content-based instead of extension-based, and makes the junction/BAM output options accept a file path for single inputs. Bumps to 2.1.0. - Add --version (CLI11 set_version_flag) sourced from a configured version.hpp generated from the CMake project VERSION, so the git tag, CMake version, --version output and conda package can't drift. A CI job fails on any CMakeLists.txt vs conda/meta.yaml version mismatch. - Detect input type by content, not extension (Galaxy names every dataset *.dat): --bam by magic bytes (BGZF/BAM, CRAM, SAM), --bed by content (BED record vs list of existing paths). Add explicit --bam_list/--bed_list; auto-detected path lists still work but warn. (Issue #2) - Fix is_file_path npos bug so bare output filenames (out.bed, out.bam) are treated as files, not directories. Move it to a shared path_utils helper and use it in OutputWriter. (Issues #1, #3, #4) - --out_original_junctions now accepts a file path for a single input and is implemented for GTF/BED (previously directory-only for BAM and a silent no-op for GTF/BED). (Issues #1, #3) - --out_filtered_bam accepts a file path for a single BAM input; fix generate_bam_output_paths multi-input parent-dir fallback. (Issue #4) - Add GitHub Actions CI (x86_64, linux-aarch64, osx-arm64) + tests for path generation and content detection (incl. a *.dat input case). - Update README output-option docs (file vs directory, the --removed_alignments_bam suffix) and add CHANGELOG. Closes #1 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
pkg-config sets HTSLIB_LIBRARIES to the bare "hts" and the directory in HTSLIB_LIBRARY_DIRS, which is not on the default linker search path on macOS (Homebrew's /opt/homebrew/lib), causing "ld: library 'hts' not found". Add the dir via target_link_directories. Surfaced by the new macos-latest CI job. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Fixes several CLI/output/packaging issues found while wrapping EASTR as a Galaxy tool, so the wrapper can drop its workarounds. Bumps to 2.1.0.
Changes
--versionflag (CLI11set_version_flag) sourced from a configuredversion.hppgenerated from the CMakeproject(... VERSION ...)— a single source of truth, so the git tag, CMake version,--versionoutput, and conda package can't drift. A CI job fails on anyCMakeLists.txtvsconda/meta.yamlmismatch. (required for Galaxy provenance)Content-based input detection (issue Fix CLI/output/packaging issues for Galaxy/Bioconda integration #2). Input type is detected by file content, not extension, so inputs work regardless of name (Galaxy names every dataset
*.dat):--bamby magic bytes (BGZF/BAM, CRAM, SAM)--bedby content (a BED record vs. a list of existing paths)--bam_list/--bed_listflags; auto-detected path lists still work but emit a deprecation warning.Output options accept a file path for single inputs (issues junction output are readin as .bed but not PATH #1, Fix --out_filtered_bam <file> creating a directory for a single BAM (2.1.1) #3, #4):
is_file_pathnposbug where bare filenames (out.bed,out.bam) were misread as directories. Moved to a sharedpath_utilshelper used byOutputWriter.--out_original_junctionsnow accepts a file path for a single input and is implemented for GTF/BED (was directory-only for BAM and a silent no-op for GTF/BED). Directory mode kept for multi-input.--out_filtered_bamaccepts a file path for a single BAM; fixed thegenerate_bam_output_pathsmulti-input parent-dir fallback.ARM64 / CI (issue #5): added GitHub Actions CI building + testing on
ubuntu-latest(x86_64),ubuntu-24.04-arm(linux-aarch64), andmacos-latest(osx-arm64). The code already had the minimap2sse2neonpath for ARM.Docs/tests: README output-option docs clarified (file vs directory, the
--removed_alignments_bam_removed_alignments.bamsuffix); new unit tests for path generation and content detection (incl. a*.datinput case);CHANGELOG.mdadded.Follow-ups (not in this PR)
v2.1.0and update thesha256inconda/meta.yaml.bioconda-recipesPR addingadditional_platforms: [linux-aarch64].Closes #1