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#include <stdio.h>
#include <string.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "dummy"
#endif
#include "main.h"
static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: maq (Mapping and Assembly with Qualities)\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
fprintf(stderr, "Usage: maq <command> [options]\n\n");
fprintf(stderr, "Key commands:\n");
fprintf(stderr, " fasta2bfa convert FASTA to BFA format\n");
fprintf(stderr, " fastq2bfq convert FASTQ to BFQ format\n");
fprintf(stderr, " map map reads to the reference\n"); // valgrind on 10AUG2007
fprintf(stderr, " mapmerge merge several alignments\n"); // valgrind on 11JUL2007
fprintf(stderr, " rmdup remove pairs with identical outer coordinates (PE)\n");
fprintf(stderr, " indelpe indel calling (PAIRED READS ONLY)\n");
fprintf(stderr, " indelsoa state-of-art homozygous indel detection\n"); // valgrind on 11JUL2007
fprintf(stderr, " assemble call the consensus\n"); // valgrind on 11JUL2007
fprintf(stderr, " glfgen generate .glz consensus\n\n");
fprintf(stderr, "Format converting:\n");
fprintf(stderr, " sol2sanger convert Solexa FASTQ to standard/Sanger FASTQ\n");
fprintf(stderr, " mapass2maq convert mapass2's map format to maq's map format\n");
fprintf(stderr, " bfq2fastq convert BFQ to FASTQ format\n\n");
fprintf(stderr, "Information extracting:\n");
fprintf(stderr, " mapview view the mapping alignment\n"); // valgrind on 11JUL2007
fprintf(stderr, " mapstat statistics about a .map file\n");
fprintf(stderr, " mapcheck a QC command\n"); // 11JUL2007: valgrind failed on "-g -O2 -m64"; passed on "-g"
fprintf(stderr, " pileup view the alignment in a 'pileup' like format\n"); // valgrind on 11JUL2007
fprintf(stderr, " cns2fq extract the consensus sequences from a CNS file\n");
fprintf(stderr, " cns2snp extract details from a CNS file at the SNP sites\n");
fprintf(stderr, " snpreg calculate the length of regions where SNPs can be called\n");
fprintf(stderr, " cns2view extract details from a CNS file at all sites\n");
fprintf(stderr, " cns2ref extract the reference sequences from a CNS file\n");
fprintf(stderr, " cns2win extract details in a window\n\n");
fprintf(stderr, "SOLiD related commands:\n");
fprintf(stderr, " fasta2csfa convert FASTA to colour-space FASTA\n");
fprintf(stderr, " csmap2nt convert colour-space .map to nucleotide .map\n\n");
// fprintf(stderr, " cns2cssnp SNP calling for AB SOLiD\n\n");
fprintf(stderr, "Simulation related commands:\n");
fprintf(stderr, " fakemut simulate references: randomly generate mutations\n");
fprintf(stderr, " simutrain train parameters for simulation\n");
fprintf(stderr, " simulate simulate reads: randomly generate sequencing errors\n");
fprintf(stderr, " simucns evaluate consensus based on simulation\n");
fprintf(stderr, " simustat evaluate alignment based on simulation\n\n");
fprintf(stderr, "Miscellaneous/advanced utilities:\n");
fprintf(stderr, " submap extract a region from a map file\n");
fprintf(stderr, " mapvalidate validate a .map file\n");
// fprintf(stderr, " rbcc reference based consensus calling\n");
fprintf(stderr, " subpos extract a subset of positions\n");
fprintf(stderr, " eland2maq convert eland alignment to maq\n");
fprintf(stderr, " export2maq convert Solexa's export alignment to maq\n");
fprintf(stderr, " novo2maq convert novoalign/novopaired alignment to maq\n");
#ifdef MAQ_SHOW_EXPERIMENTAL
fprintf(stderr, " abpair show the abnormal pairs (EXPERIMENTAL)\n");
fprintf(stderr, " paircov paired coverage (EXPERIMENTAL)\n");
fprintf(stderr, " altchr change reference according to SNPs (EXPERIMENTAL)\n");
#endif
fprintf(stderr, "\n");
return 1;
}
int main(int argc, char *argv[])
{
if (argc < 2) return usage();
if (strcmp(argv[1], "fasta2bfa") == 0) return ma_fasta2bfa(argc-1, argv+1);
else if (strcmp(argv[1], "fastq2bfq") == 0) return ma_fastq2bfq(argc-1, argv+1);
else if (strcmp(argv[1], "map") == 0) return ma_match(argc-1, argv+1);
else if (strcmp(argv[1], "mapmerge") == 0) return ma_mapmerge(argc-1, argv+1);
else if (strcmp(argv[1], "indelpe") == 0) return maq_indelpe(argc-1, argv+1);
else if (strcmp(argv[1], "indelsoa") == 0) return ma_indelsoa(argc-1, argv+1);
else if (strcmp(argv[1], "assemble") == 0) return ma_assemble(argc-1, argv+1);
else if (strcmp(argv[1], "glfgen") == 0) return maq_glfgen(argc-1, argv+1);
else if (strcmp(argv[1], "sol2sanger") == 0) return ma_sol2sanger(argc-1, argv+1);
else if (strcmp(argv[1], "mapass2maq") == 0) return ma_mapass2maq(argc-1, argv+1);
else if (strcmp(argv[1], "bfq2fastq") == 0) return ma_bfq2fastq(argc-1, argv+1);
else if (strcmp(argv[1], "mapview") == 0) return ma_mapview(argc-1, argv+1);
else if (strcmp(argv[1], "mapcheck") == 0) return ma_mapcheck(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) return ma_pileup(argc-1, argv+1);
else if (strcmp(argv[1], "cns2ref") == 0) return ma_cns2ref(argc-1, argv+1);
else if (strcmp(argv[1], "cns2fq") == 0) return ma_cns2fq(argc-1, argv+1);
else if (strcmp(argv[1], "cns2snp") == 0) return ma_cns2snp(argc-1, argv+1);
else if (strcmp(argv[1], "snpreg") == 0) return ma_snpreg(argc-1, argv+1);
else if (strcmp(argv[1], "cns2view") == 0) return ma_cns2view(argc-1, argv+1);
else if (strcmp(argv[1], "cns2win") == 0) return ma_cns2win(argc-1, argv+1);
else if (strcmp(argv[1], "fasta2csfa") == 0) return ma_fasta2csfa(argc-1, argv+1);
else if (strcmp(argv[1], "csmap2nt") == 0) return maq_csmap2nt(argc-1, argv+1);
else if (strcmp(argv[1], "cns2cssnp") == 0) return ma_cns2cssnp(argc-1, argv+1);
else if (strcmp(argv[1], "fakemut") == 0) return ma_fakemut(argc-1, argv+1);
else if (strcmp(argv[1], "simutrain") == 0) return maq_simutrain(argc-1, argv+1);
else if (strcmp(argv[1], "simulate") == 0) return maq_simulate(argc-1, argv+1);
else if (strcmp(argv[1], "simucns") == 0) return maq_simucns(argc-1, argv+1);
else if (strcmp(argv[1], "simustat") == 0) return maq_simustat(argc-1, argv+1);
else if (strcmp(argv[1], "match") == 0) return ma_match(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return maq_rmdup(argc-1, argv+1);
else if (strcmp(argv[1], "submap") == 0) return maq_submap(argc-1, argv+1);
else if (strcmp(argv[1], "mapvalidate") == 0) return ma_mapvalidate(argc-1, argv+1);
else if (strcmp(argv[1], "rbcc") == 0) return ma_rbcc(argc-1, argv+1);
else if (strcmp(argv[1], "mapstat") == 0) return ma_mapstat(argc-1, argv+1);
else if (strcmp(argv[1], "subpos") == 0) return ma_subpos(argc-1, argv+1);
else if (strcmp(argv[1], "eland2maq") == 0) return maq_eland2maq(argc-1, argv+1);
else if (strcmp(argv[1], "export2maq") == 0) return maq_export2maq(argc-1, argv+1);
else if (strcmp(argv[1], "novo2maq") == 0) return maq_novo2maq(argc-1, argv+1);
else if (strcmp(argv[1], "abpair") == 0) return ma_abpair(argc-1, argv+1);
else if (strcmp(argv[1], "paircov") == 0) return ma_paircov(argc-1, argv+1);
else if (strcmp(argv[1], "altchr") == 0) return ma_altchr(argc-1, argv+1);
else if (strcmp(argv[1], "catfilter") == 0) return maq_catfilter(argc-1, argv+1);
else if (strcmp(argv[1], "breakpair") == 0) return maq_breakpair(argc-1, argv+1);
else {
fprintf(stderr, "ERROR: unrecognized command '%s'\n", argv[1]);
return 2;
}
return 0;
}
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