#!/usr/bin/make -f

export DH_VERBOSE=1

export DEB_BUILD_MAINT_OPTIONS = hardening=+all

include /usr/share/dpkg/default.mk

mandir := $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
bindir := $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin

%:
	dh $@

override_dh_auto_configure:
	./reconf
	dh_auto_configure

override_dh_install:
	dh_install
	rm --recursive $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/aclocal

override_dh_installchangelogs:
	dh_installchangelogs -k NEWS

# Does not help to detect the dependencies for substitution variable ${perl:Depends} :-(
#override_dh_perl:
#	dh_perl /usr/bin

override_dh_installman:
	mkdir -p $(mandir)
	# The name strings are obtained from
	#   http://hannonlab.cshl.edu/fastx_toolkit/ (Section "Available Tools")
	# and
	#   http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='changes the width of sequences line in a FASTA file' \
	   $(bindir)/fasta_formatter > $(mandir)/fasta_formatter.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='Convets FASTA sequences from/to RNA/DNA' \
	   $(bindir)/fasta_nucleotide_changer > $(mandir)/fasta_nucleotide_changer.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name="Masks nucleotides with 'N' (or other character) based on quality" \
	   $(bindir)/fastq_masker > $(mandir)/fastq_masker.1

	# hmmmm: The tool `fasta_quality_converter` was NOT described at the URLs above
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='Converts sequences based on quality' \
	   $(bindir)/fastq_quality_converter > $(mandir)/fastq_quality_converter.1

	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='Filters sequences based on quality' \
	   $(bindir)/fastq_quality_filter > $(mandir)/fastq_quality_filter.1

# hmmmm: For some very strange reason this conversion fails
#
#	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
#	   --name='Filters sequences based on quality' \
#	   $(bindir)/fastq_quality_trimmer > $(mandir)/fastq_quality_trimmer .1
# lets simply use what works perfectly at command line
	dh_installman debian/fastq_quality_trimmer.1

	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='Convert FASTQ files to FASTA files' \
	   $(bindir)/fastq_to_fasta > $(mandir)/fastq_to_fasta.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTQ/A Artifacts Filter' \
	   $(bindir)/fastx_artifacts_filter > $(mandir)/fastx_artifacts_filter.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Clipper' \
	   $(bindir)/fastx_clipper > $(mandir)/fastx_clipper.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Collapser' \
	   $(bindir)/fastx_collapser > $(mandir)/fastx_collapser.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTX Statistics' \
	   $(bindir)/fastx_quality_stats > $(mandir)/fastx_quality_stats.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Renamer' \
	   $(bindir)/fastx_renamer > $(mandir)/fastx_renamer.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTQ/A Reverse Complement' \
	   $(bindir)/fastx_reverse_complement > $(mandir)/fastx_reverse_complement.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Trimmer' \
	   $(bindir)/fastx_trimmer > $(mandir)/fastx_trimmer.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Uncollapser' \
	   $(bindir)/fastx_uncollapser > $(mandir)/fastx_uncollapser.1

	# Perl scripts add the full path to usage advise which needs to be removed
	# The script fasta_clipping_histogram.pl does not feature a '-h' option
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' -h '' \
	   --name='Create a Linker Clipping Information Histogram' \
	   $(bindir)/fasta_clipping_histogram.pl | \
	   sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \
	   > $(mandir)/fasta_clipping_histogram.pl.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTX Barcode Splitter' \
	   $(bindir)/fastx_barcode_splitter.pl | \
	   sed -e 's?^usage: .*\([^/]\+\.pl\)?usage: \1?' \
	   > $(mandir)/fastx_barcode_splitter.pl.1

	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='Solexa-Quality BoxPlot plotter' \
	   $(bindir)/fastq_quality_boxplot_graph.sh > $(mandir)/fastq_quality_boxplot_graph.sh.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Nucleotide Distribution Plotter' \
	   $(bindir)/fastx_nucleotide_distribution_graph.sh > $(mandir)/fastx_nucleotide_distribution_graph.sh.1
	help2man --no-info --no-discard-stderr --version-string='$(DEB_VERSION_UPSTREAM)' --help-option='-h' \
	   --name='FASTA/Q Nucleotide Distribution Plotter' \
	   $(bindir)/fastx_nucleotide_distribution_line_graph.sh > $(mandir)/fastx_nucleotide_distribution_line_graph.sh.1

	for man in `find $(mandir) "*.1"` ; do cat debian/manpages_see_also >> $$man ; done