add an option alias -O for the old obi format

Makefile

@@ -1,106 +1,53 @@
-MODULE   = $(shell env GO111MODULE=on $(GO) list -m)
+GOCMD=go
-DATE    ?= $(shell date +%FT%T%z)
+GOBUILD=$(GOCMD) build
-VERSION ?= $(shell git describe --tags --always --dirty --match=v* 2> /dev/null || \
+GOCLEAN=$(GOCMD) clean
-			cat $(CURDIR)/.version 2> /dev/null || echo v0)
+GOTEST=$(GOCMD) test
-PKGS     = $(or $(PKG),$(shell env GO111MODULE=on $(GO) list ./...))
+GOGET=$(GOCMD) get
-TESTPKGS = $(shell env GO111MODULE=on $(GO) list -f \
-			'{{ if or .TestGoFiles .XTestGoFiles }}{{ .ImportPath }}{{ end }}' \
-			$(PKGS))
-BIN      = $(CURDIR)/bin
 
-GO      = go
+BUILD_DIR=build
-TIMEOUT = 15
+OBITOOLS_PREFIX:=g
-V = 0
-Q = $(if $(filter 1,$V),,@)
-M = $(shell printf "\033[34;1m▶\033[0m")
 
-export GO111MODULE=on
+PACKAGES_SRC:= $(wildcard pkg/*/*.go pkg/*/*/*.go)
+PACKAGE_DIRS:=$(sort $(patsubst %/,%,$(dir $(PACKAGES_SRC))))
+PACKAGES:=$(notdir $(PACKAGE_DIRS))
+
+OBITOOLS_SRC:= $(wildcard cmd/obitools/*/*.go)
+OBITOOLS_DIRS:=$(sort $(patsubst %/,%,$(dir $(OBITOOLS_SRC))))
+OBITOOLS:=$(notdir $(OBITOOLS_DIRS))
 
 .PHONY: all
-all: fmt lint | $(BIN) ; $(info $(M) building executable…) @ ## Build program binary
-	$Q $(GO) build \
-		-tags release \
-		-ldflags '-X $(MODULE)/cmd.Version=$(VERSION) -X $(MODULE)/cmd.BuildDate=$(DATE)' \
-		-o $(BIN)/$(basename $(MODULE)) main.go
 
-# Tools
+define MAKE_PKG_RULE
+pkg-$(notdir $(1)): $(1)
+	@echo -n - Building package $(notdir $(1))...
+	@$(GOBUILD) ./$(1) \
+	    2> pkg-$(notdir $(1)).log \
+		|| cat pkg-$(notdir $(1)).log
+	@rm -f pkg-$(notdir $(1)).log
+	@echo Done.
+endef
 
-$(BIN):
+define MAKE_OBITOOLS_RULE
-	@mkdir -p $@
+$(OBITOOLS_PREFIX)$(notdir $(1)): $(BUILD_DIR) $(1)
-$(BIN)/%: | $(BIN) ; $(info $(M) building $(PACKAGE)…)
+	@echo -n - Building obitool $(notdir $(1))...
-	$Q tmp=$$(mktemp -d); \
+	@$(GOBUILD)  -o $(BUILD_DIR)/$(OBITOOLS_PREFIX)$(notdir $(1)) ./$(1) \
-	   env GO111MODULE=off GOPATH=$$tmp GOBIN=$(BIN) $(GO) get $(PACKAGE) \
+	             2> $(OBITOOLS_PREFIX)$(notdir $(1)).log \
-		|| ret=$$?; \
+				 || cat $(OBITOOLS_PREFIX)$(notdir $(1)).log
-	   rm -rf $$tmp ; exit $$ret
+	@rm -f $(OBITOOLS_PREFIX)$(notdir $(1)).log
+	@echo Done.
+endef
 
-GOLINT = $(BIN)/golint
-$(BIN)/golint: PACKAGE=golang.org/x/lint/golint
 
-GOCOV = $(BIN)/gocov
+all: obitools
-$(BIN)/gocov: PACKAGE=github.com/axw/gocov/...
 
-GOCOVXML = $(BIN)/gocov-xml
+packages: $(patsubst %,pkg-%,$(PACKAGES))
-$(BIN)/gocov-xml: PACKAGE=github.com/AlekSi/gocov-xml
+obitools: $(patsubst %,$(OBITOOLS_PREFIX)%,$(OBITOOLS)) 
 
-GO2XUNIT = $(BIN)/go2xunit
+$(BUILD_DIR):
-$(BIN)/go2xunit: PACKAGE=github.com/tebeka/go2xunit
+	mkdir -p $@
 
-# Tests
 
-TEST_TARGETS := test-default test-bench test-short test-verbose test-race
+$(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P))))
-.PHONY: $(TEST_TARGETS) test-xml check test tests
-test-bench:   ARGS=-run=__absolutelynothing__ -bench=. ## Run benchmarks
-test-short:   ARGS=-short        ## Run only short tests
-test-verbose: ARGS=-v            ## Run tests in verbose mode with coverage reporting
-test-race:    ARGS=-race         ## Run tests with race detector
-$(TEST_TARGETS): NAME=$(MAKECMDGOALS:test-%=%)
-$(TEST_TARGETS): test
-check test tests: fmt lint ; $(info $(M) running $(NAME:%=% )tests…) @ ## Run tests
-	$Q $(GO) test -timeout $(TIMEOUT)s $(ARGS) $(TESTPKGS)
 
-test-xml: fmt lint | $(GO2XUNIT) ; $(info $(M) running xUnit tests…) @ ## Run tests with xUnit output
+$(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P))))
-	$Q mkdir -p test
-	$Q 2>&1 $(GO) test -timeout $(TIMEOUT)s -v $(TESTPKGS) | tee test/tests.output
-	$(GO2XUNIT) -fail -input test/tests.output -output test/tests.xml
 
-COVERAGE_MODE    = atomic
-COVERAGE_PROFILE = $(COVERAGE_DIR)/profile.out
-COVERAGE_XML     = $(COVERAGE_DIR)/coverage.xml
-COVERAGE_HTML    = $(COVERAGE_DIR)/index.html
-.PHONY: test-coverage test-coverage-tools
-test-coverage-tools: | $(GOCOV) $(GOCOVXML)
-test-coverage: COVERAGE_DIR := $(CURDIR)/test/coverage.$(shell date -u +"%Y-%m-%dT%H:%M:%SZ")
-test-coverage: fmt lint test-coverage-tools ; $(info $(M) running coverage tests…) @ ## Run coverage tests
-	$Q mkdir -p $(COVERAGE_DIR)
-	$Q $(GO) test \
-		-coverpkg=$$($(GO) list -f '{{ join .Deps "\n" }}' $(TESTPKGS) | \
-					grep '^$(MODULE)/' | \
-					tr '\n' ',' | sed 's/,$$//') \
-		-covermode=$(COVERAGE_MODE) \
-		-coverprofile="$(COVERAGE_PROFILE)" $(TESTPKGS)
-	$Q $(GO) tool cover -html=$(COVERAGE_PROFILE) -o $(COVERAGE_HTML)
-	$Q $(GOCOV) convert $(COVERAGE_PROFILE) | $(GOCOVXML) > $(COVERAGE_XML)
-
-.PHONY: lint
-lint: | $(GOLINT) ; $(info $(M) running golint…) @ ## Run golint
-	$Q $(GOLINT) -set_exit_status $(PKGS)
-
-.PHONY: fmt
-fmt: ; $(info $(M) running gofmt…) @ ## Run gofmt on all source files
-	$Q $(GO) fmt $(PKGS)
-
-# Misc
-
-.PHONY: clean
-clean: ; $(info $(M) cleaning…)	@ ## Cleanup everything
-	@rm -rf $(BIN)
-	@rm -rf test/tests.* test/coverage.*
-
-.PHONY: help
-help:
-	@grep -hE '^[ a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | \
-		awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-17s\033[0m %s\n", $$1, $$2}'
-
-.PHONY: version
-version:
-	@echo $(VERSION)

go.mod

@@ -4,6 +4,7 @@ go 1.17
 
 require (
 	github.com/DavidGamba/go-getoptions v0.25.3
+	github.com/PaesslerAG/gval v1.1.2
 	github.com/goccy/go-json v0.9.4
 	github.com/schollz/progressbar/v3 v3.8.6
 	github.com/tevino/abool/v2 v2.0.1

go.sum

@@ -1,5 +1,8 @@
 github.com/DavidGamba/go-getoptions v0.25.3 h1:lSPcMkwWvVZU05C+Uz4DKnKN5wz4bcD1QvJ/QHCRexo=
 github.com/DavidGamba/go-getoptions v0.25.3/go.mod h1:qLaLSYeQ8sUVOfKuu5JT5qKKS3OCwyhkYSJnoG+ggmo=
+github.com/PaesslerAG/gval v1.1.2 h1:EROKxV4/fAKWb0Qoj7NOxmHZA7gcpjOV9XgiRZMRCUU=
+github.com/PaesslerAG/gval v1.1.2/go.mod h1:Fa8gfkCmUsELXgayr8sfL/sw+VzCVoa03dcOcR/if2w=
+github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=

pkg/obitools/obiconvert/options.go

@@ -54,6 +54,7 @@ func OutputOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__output_fastjson_format__, "output-json-header", false,
 		options.Description("output FASTA/FASTQ title line annotations follow json format."))
 	options.BoolVar(&__output_fastobi_format__, "output-OBI-header", false,
+		options.Alias("O"),
 		options.Description("output FASTA/FASTQ title line annotations follow OBI format."))
 
 	options.BoolVar(&__output_solexa_quality__, "solexa-output", false,

pkg/obitools/obipairing/options.go

@@ -29,7 +29,6 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 		options.Alias("D"),
 		options.Description("Length added to the fast detected overlap for the precise alignement"))
 	options.IntVar(&_MinOverlap, "min-overlap", _MinOverlap,
-		options.Alias("O"),
 		options.Description("Minimum ovelap between both the reads to consider the aligment"))
 	options.Float64Var(&_MinIdentity, "min-identity", _MinIdentity,
 		options.Alias("X"),