Unify G and T parameters in the make file

bin/goldrush

@@ -27,7 +27,6 @@ x=10
 h=3
 j=48
 s=1011011110110111101101
-T=3000000000 
 r=0.9 
 M=5
 p1=w$(w)_x$(x)
@@ -41,7 +40,6 @@ t=8
 # Default Tigmint parameters
 span=2
 dist=1000
-G=3e9
 cut=250
 
 # Default ntLink parameters
@@ -88,7 +86,7 @@ time=command memusg -t -o $@.time
 endif
 endif
 
-.PHONY: help run clean wp2-tigmint-ntlink wp2-racon workpackage2 racon wp2-ntLink ntLink-with-wp2 wp2-tigmint tigmint wp2-tigmint-ntlink1 ntLink-with-tigmint wp2-tigmint-ntLink2 ntLink2 wp2-tigmint-ntLink3 ntLink3 wp2-tigmint-ntLink4 ntLink4 wp2-tigmint-ntLink5 ntLink5 wp2-tigmint-ntJoin ntJoin
+.PHONY: help run clean wp2-tigmint-ntlink wp2-racon workpackage2 racon wp2-ntLink ntLink-with-wp2 wp2-tigmint tigmint wp2-tigmint-ntlink1 ntLink-with-tigmint wp2-tigmint-ntLink2 ntLink2 wp2-tigmint-ntLink3 ntLink3 wp2-tigmint-ntLink4 ntLink4 wp2-tigmint-ntLink5 ntLink5 wp2-tigmint-ntJoin ntJoin check-G
 .DELETE_ON_ERROR:
 .SECONDARY:
 
@@ -114,6 +112,7 @@ help:
 	@echo ""
 	@echo "	General options (required):"
 	@echo "	reads			read name [reads]. File must have .fq.gz or .fa.gz extension"
+	@echo "	G			haploid genome size (bp) for calculating span parameter and target for generating silver paths(e.g. '3e9' for human genome). used in GoldRush-Path and Timignt. Required [3e9]"
 	@echo ""
 	@echo "	General options (optional):"
 	@echo "	t			number of threads for scaffolding and correction tools [8]"
@@ -131,16 +130,14 @@ help:
 	@echo "	x			threshold for number of hits in miBF for a given frame to be considered assigned [10]"	
 	@echo "	h			the number of seed patterns to use [3]"
 	@echo "	j			number of threads to use [48]"
-	@echo "	s       		spaced seed design [1011011110110111101101]"
-	@echo "	T			total genome size [3000000000]"	
+	@echo "	s       		spaced seed design [1011011110110111101101]"	
 	@echo "	M			maximum number of silver paths to generate [5]"
 	@echo "	r			ratio of full genome in golden path [0.9]"
 	@echo "	p1			prefix to use for the silver paths [w$(w)_x$(x)]"
 	@echo ""
 	@echo "	Tigmint options:"
 	@echo "	span			min number of spanning molecules to be considered correctly assembled [2]"
 	@echo "	dist			maximum distance between alignments to be considered the same molecule [1000]"
-	@echo "	G			haploid genome size (bp) for calculating span parameter (e.g. '3e9' for human genome). Required when span=auto [3e9]"
 	@echo ""
 	@echo "	ntLink options:"
 	@echo "	k_ntLink		k-mer size for minimizers [64]"
@@ -173,9 +170,14 @@ wp2-tigmint-ntJoin: ntJoin
 ntlink_targets = $(shell for i in `seq 2 $(rounds)`; do printf "$(p2)_golden_path_1.racon-polished.span$(span).dist$(dist).tigmint.fa.k$(k_ntLink).w$(w_ntLink)"; for j in `seq 1 $$i`; do printf ".ntLink"; done; printf ".fa "; done)
 wp2-tigmint-ntLink: ntLink1 $(ntlink_targets) ntLink_softlink
 
+check-G:
+ifndef G
+	$(error G is undefined. Try goldrush help for more information)
+endif
+
 
 # Run workpackage2
-workpackage2: $(p2)_golden_path_1.fq
+workpackage2: $(p2)_golden_path_1.fq check-G
 
 $(p2)_golden_path_1.fq: $(p1)_golden_path_all.fq 
 	$(time) goldrush-path  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p2) -i $(p1)_golden_path_all.fq -h $(h) -j $(j) -P $(P) -x$(x) -s $(s) -m 0 
@@ -185,7 +187,7 @@ $(p1)_golden_path_all.fq: $(p1)_golden_path_$(M).fq
 	cat $(p1)_golden_path_*.fq > $(p1)_golden_path_all.fq
 
 $(p1)_golden_path_$(M).fq: $(long_reads)
-	$(time) goldrush-path  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p1) -i $(long_reads)  -h $(h) -j $(j) -x$(x) -P $(P) -s $(s) -T $(T) -r $(r) --new_temp_mode -M $(M) -m $(m)
+	$(time) goldrush-path  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p1) -i $(long_reads)  -h $(h) -j $(j) -x$(x) -P $(P) -s $(s) -T $(G) -r $(r) --new_temp_mode -M $(M) -m $(m)
 
 
 # Run racon 
@@ -210,7 +212,7 @@ ntLink-with-wp2: $(p2)_golden_path_1.racon-polished.fa.k$(k_ntLink).w$(w_ntLink)
 
 
 # Run tigmint after wp2
-tigmint: $(p2)_golden_path_1.racon-polished.span$(span).dist$(dist).tigmint.fa
+tigmint: $(p2)_golden_path_1.racon-polished.span$(span).dist$(dist).tigmint.fa check-G
 
 $(p2)_golden_path_1.racon-polished.span$(span).dist$(dist).tigmint.fa: $(p2)_golden_path_1.racon-polished.cut$(cut).tigmint.fa
 	ln -sf $< $@

goldrush_path/opt.cpp

@@ -1,14 +1,14 @@
 #include "opt.hpp"
-
+#include <cmath>
 #include <iostream>
 
 namespace opt {
 
 size_t assigned_max = 5;
 size_t unassigned_min = 5;
 size_t tile_length = 1000;
-size_t genome_size = 0;
-size_t target_size = 0;
+uint64_t genome_size = 0;
+uint64_t target_size = 0;
 size_t kmer_size = 0;
 size_t weight = 0;
 size_t min_length = 5000;
@@ -132,7 +132,7 @@ process_options(int argc, char** argv)
         opt::tile_length = strtoul(optarg, &end, 10);
         break;
       case 'T':
-        opt::target_size = strtoul(optarg, &end, 10);
+        opt::target_size = (uint64_t)strtod(optarg, &end);
         break;
       case 'u': {
         opt::unassigned_min = strtoul(optarg, &end, 10);

goldrush_path/opt.hpp

@@ -11,8 +11,8 @@ extern size_t assigned_max;
 extern size_t unassigned_min;
 extern size_t tile_length;
 extern size_t block_size;
-extern size_t genome_size;
-extern size_t target_size;
+extern uint64_t genome_size;
+extern uint64_t target_size;
 extern size_t kmer_size;
 extern uint32_t phred_min;
 extern uint32_t phred_delta;