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#!/usr/bin/make -rRf
SHELL=/bin/bash
#------------------------------------------------------------
# test input/output files
#------------------------------------------------------------
# target seq for alignments
ref_url:=http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/genome.fasta
ref:=ref.fa
test_ref=test_ref.fa
# query seqs for alignments
reads_url:=http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz
reads=reads.fq.gz
test_reads=test_reads.fq
# output alignment files
dida_wrapper_sam=dida_wrapper.sam
abyss_map_sam=abyss_map.sam
#------------------------------------------------------------
# params
#------------------------------------------------------------
# number of MPI tasks
np?=3
# number of threads per task
j?=1
# min align length
l?=20
# num of reads to align
n?=10000
#------------------------------------------------------------
# special targets
#------------------------------------------------------------
.PHONY: clean dida_wrapper_test
default: dida_wrapper_test
clean:
rm -f $(dida_wrapper_sam) $(abyss_map_sam) ref-* *.lines $(test_reads)
#------------------------------------------------------------
# downloading/building test input data
#------------------------------------------------------------
# download ref
$(ref):
curl $(ref_url) > $@
# split ref into chunks of 100,000bp or less
$(test_ref): $(ref)
fold -w 100000 $^ | awk '{print ">"i++; print $$0}' > $@
# download some reads
$(reads):
curl $(reads_url) > $@
# extract first $n reads
$(test_reads): $(reads)
zcat $(reads) | paste - - - - | head -$n | \
tr '\t' '\n' > $@
#------------------------------------------------------------
# running DIDA/abyss-map
#------------------------------------------------------------
$(dida_wrapper_sam): $(test_reads) $(test_ref)
abyss-dida-wrapper -l$l -j$j $(ALIGNER_OPTIONS) -d'$(DIDA_OPTIONS)' $^ > $@
$(abyss_map_sam): $(test_reads) $(test_ref)
abyss-map --order -l$l -j$j $^ > $@
#------------------------------------------------------------
# tests
#------------------------------------------------------------
dida_wrapper_test: $(abyss_map_sam) $(dida_wrapper_sam)
compare-sam $(abyss_map_sam) $(dida_wrapper_sam)
@echo $@": PASSED!"
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