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#include "version.h"
#include "assemblygraph.h"
#include "assembly_stream_fasta.h"
#include "assembly_sanger_project.h"
#include "kmer_glib_index.h"
#include "kmer_hash.h"
#include "assemblystats.h"
#include "graphmanager.h"
char * program_name = "pathwise";
void show_help(FILE * ofp)
{
fprintf(ofp,"%s (%s)\n",program_name,VERSION_NUMBER);
fprintf(ofp,"Graph statistics display\n");
fprintf(ofp," -[no]stat_raw show stats just after sequence load\n");
fprintf(ofp," -[no]stat_error show stats just after error manip\n");
fprintf(ofp," -[no]stat_tangle show stats just after de-tangling\n");
fprintf(ofp,"Graph manipulation\n");
fprintf(ofp," -[no]error_free reads are error free. (off by default)\n");
fprintf(ofp,"Read input type\n");
fprintf(ofp," -readstream [fasta/sanger] Read input type (fasta by default)\n");
fprintf(ofp," -readmax [number] maximum reads to use (good for debugging)\n");
show_help_GraphErrorPara(ofp);
show_help_DepthPara(ofp);
show_help_AssemblyOutputPara(ofp);
fprintf(ofp,"Kmer options\n");
fprintf(ofp," -kmer [15] kmer size (15 is max)\n");
fprintf(ofp," -[no]hash use optimised hash (true)\n");
show_standard_options(ofp);
}
void show_version(FILE * ofp)
{
fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
fprintf(ofp,"The source code is copyright (c) EBI 2003\n");
fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
fprintf(ofp,"Credits: Ewan Birney <birney@ebi.ac.uk> wrote the core code.\n");
exit(63);
}
int main(int argc,char ** argv)
{
boolean show_stats_before = 0;
boolean show_stats_error = 0;
boolean show_stats_tangle = 0;
boolean show_fasta_contigs = 1;
boolean use_hash = 1;
boolean no_error = 0;
int readmax = 0;
int kmer = 15;
int load;
int cycle_count;
GraphErrorPara * gep;
DepthPara * dp;
AssemblyGraph * ag;
AssemblyGraphStats * astat;
AssemblySequenceStream * as;
AssemblyOutputPara * aop;
Assembly * assem;
FILE * ifp;
KmerIndexInterface * kii;
char * streamtype = NULL;
gep = new_GraphErrorPara_from_argv(&argc,argv);
dp = new_DepthPara_from_argv(&argc,argv);
aop = new_AssemblyOutputPara_from_argv(&argc,argv);
strip_out_integer_argument(&argc,argv,"kmer",&kmer);
strip_out_boolean_def_argument(&argc,argv,"hash",&use_hash);
strip_out_boolean_def_argument(&argc,argv,"error_free",&no_error);
strip_out_boolean_def_argument(&argc,argv,"stat_raw",&show_stats_before);
strip_out_boolean_def_argument(&argc,argv,"stat_error",&show_stats_error);
strip_out_boolean_def_argument(&argc,argv,"stat_tangle",&show_stats_tangle);
strip_out_integer_argument(&argc,argv,"readmax",&readmax);
streamtype = strip_out_assigned_argument(&argc,argv,"readstream");
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc == 1 ) {
show_help(stdout);
exit(1);
}
if( streamtype == NULL || strcmp(streamtype,"fasta") == 0 ) {
ifp = openfile(argv[1],"r");
as = plain_fasta_AssemblySequenceStream(ifp);
} else if( strcmp(streamtype,"sanger") == 0 ) {
as = new_sanger_project_AssemblySequenceStream(argv[1],"1c");
} else {
fatal("Bad stream type [%s]",streamtype);
}
if( use_hash == 0 ) {
kii = new_interface_KmerGlibIndex(kmer);
} else {
kii = new_KmerHashIndex(kmer);
}
ag = new_AssemblyGraph(kii,500);
load = load_AssemblyGraph(ag,as,readmax);
if( show_stats_before ) {
astat = new_AssemblyGraphStats(ag);
show_AssemblyGraphStats(astat,10,10,stdout);
free_AssemblyGraphStats(astat);
}
cycle_count = find_single_cycles_AssemblyGraph(ag);
fprintf(stderr,"Found %d cycles\n",cycle_count);
cycle_count = find_di_cycles_AssemblyGraph(ag);
fprintf(stderr,"Found %d dicycles\n",cycle_count);
/* handle errors */
if( no_error == 0 ) {
find_simple_errors_AssemblyGraph(ag,gep);
}
if( show_stats_error ) {
astat = new_AssemblyGraphStats(ag);
show_AssemblyGraphStats(astat,10,10,stdout);
free_AssemblyGraphStats(astat);
}
/* handle tangles */
find_and_resolve_tangles_AssemblyGraph(ag);
/* now resolve internal tangles */
/* find_and_resolve_tangles_AssemblyGraph_Para(ag,dp,1);*/
if( show_stats_tangle ) {
astat = new_AssemblyGraphStats(ag);
show_AssemblyGraphStats(astat,10,10,stdout);
free_AssemblyGraphStats(astat);
}
/* handle supertangles */
/* find_and_jump_supertangles_AssemblyGraph(ag);*/
if( show_fasta_contigs ) {
assem = Assembly_from_AssemblyGraph(ag,dp);
dump_contigs_as_fasta_Assembly(assem,aop,stdout);
}
return 0;
}
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