cramore.cpp

//#include <iostream>
//#include <string>
//#include <map>
//#include <vector>
//#include <ctime>
//#include <cstdlib>
//#ifdef _OPENMP
//  #include <omp.h>
//#else
//  #define omp_get_thread_num() 0
//#endif  

#include "cramore.h"
#include "commands.h"

//#include "htslib/sam.h"
//#include "htslib/faidx.h"
//#include "htslib/kseq.h"
//#include "htslib/khash.h"
//#include "dropseq.h"
#include "utils.h"

KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
typedef khash_t(vdict) vdict_t;


int32_t cmdCramDemuxlet(int32_t argc, char** argv);
int32_t cmdCramFreemuxlet(int32_t argc, char** argv);
int32_t cmdCramFreemux2(int32_t argc, char** argv);
int32_t cmdCramDigitalPileup(int32_t argc, char** argv);
int32_t cmdPlpMakeDGEMatrix(int32_t argc, char** argv);


int32_t main(int32_t argc, char** argv) {
  commandList cl;

  BEGIN_LONG_COMMANDS(longCommandlines)
    
    LONG_COMMAND_GROUP("Single cell analysis", NULL)
    LONG_COMMAND("demuxlet", &cmdCramDemuxlet, "Deconvolute sample identify of droplet-based sc-RNAseq")
    LONG_COMMAND("freemuxlet-old", &cmdCramFreemuxlet, "Genotype-free deconvolution of sc-RNAseq (deprecated)")
    LONG_COMMAND("freemuxlet", &cmdCramFreemux2, "Genotype-free deconvolution of sc-RNAseq")    
    LONG_COMMAND("dsc-pileup", &cmdCramDigitalPileup, "Produce pileup of dsc-RNAseq")    
    LONG_COMMAND("plp-make-dge-matrix", &cmdPlpMakeDGEMatrix, "Make Digital Expression Matrix from Digital Pileups")
  END_LONG_COMMANDS();

  cl.Add(new longCommands("Available Commands", longCommandlines));
  
  if ( argc < 2 ) {
    printf("[freemuxlet] -- Genotyping-free deconvolution tool for multiplexed single cell experiment over multiple individuals\n\n");
    fprintf(stderr, " Copyright (c) 2009-2019 by Hyun Min Kang and Fan Zhang\n");
    fprintf(stderr, " Licensed under the Apache License v2.0 http://www.apache.org/licenses/\n\n");    
    fprintf(stderr, "To run a specific command      : %s [command] [options]\n",argv[0]);
    fprintf(stderr, "For detailed instructions, run : %s --help\n",argv[0]);        
    cl.Status();
    return 1;
  }
  else {
    if ( strcmp(argv[1],"--help") == 0 ) {
      cl.HelpMessage();
    }
    else {
      return cl.Read(argc, argv);
    }
  }
  return 0;
}