qbcf.cpp

#include "qbcf.h"
#include "qgenlib/commands.h"
#include "qgenlib/qgen_utils.h"

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

  BEGIN_LONG_COMMANDS(longCommandlines)
    LONG_COMMAND_GROUP("QGEN-based BCF tools", NULL)
    LONG_COMMAND("cally", &qbcf_callY, "Call chrY variants from AD-present BCFs")

    LONG_COMMAND_GROUP("Miscellaneous tools", NULL)
    LONG_COMMAND("test-qgenlib", &qbcf_test_qgenlib, "Test basic functionalities in qgenlib")
  END_LONG_COMMANDS();

  cl.Add(new longCommands("Available Commands", longCommandlines));
  
  if ( argc < 2 ) {
    printf("[qbcf] -- spatial transcriptomics utilities\n\n");
    fprintf(stderr, " Copyright (c) 2022 by Hyun Min Kang\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;
}