int index_main(SgrepData *sgrep,int argc, char *argv[]) {
int end_options;
IndexOptions options;
FileList *file_list=NULL;
set_default_index_options(sgrep,&options);
/*
* Get the command line options
*/
end_options=parse_index_options(&options,argv);
if (end_options==SGREP_ERROR) {
/* There was error. Display usage information */
index_usage(sgrep);
goto error;
}
switch(options.index_mode) {
case IM_CREATE: {
if (argc==end_options && options.file_list_files==NULL) {
sgrep_error(sgrep,"Can't read input from stdin when indexing.\n");
sgrep_error(sgrep," Use filename '-' to force indexing from stdin.\n");
goto error;
}
if (argc>end_options) {
file_list=check_files(sgrep,argc-end_options,argv+end_options,
0,NULL);
}
options.file_list=file_list;
if (create_index(&options)==SGREP_ERROR) {
goto error;
}
break;
}
case IM_TERMS: {
if (index_query(&options,argc-end_options,argv+end_options)
==SGREP_ERROR) {
return 2;
} else {
return 0;
}
}
case IM_DONE:
return 0;
case IM_NONE:
default:
sgrep_error(sgrep,"sgindex: You have to give one of -c, -C -h\n");
index_usage(sgrep);
goto error;
}
if (file_list) delete_flist(file_list);
if (options.file_list_files) delete_flist(options.file_list_files);
return 0;
error:
if (file_list) delete_flist(file_list);
if (options.file_list_files) delete_flist(options.file_list_files);
return 2;
}
int bam_index(int argc, char *argv[])
{
int csi = 0;
int min_shift = BAM_LIDX_SHIFT;
int c;
while ((c = getopt(argc, argv, "bcm:")) >= 0)
switch (c) {
case 'b': csi = 0; break;
case 'c': csi = 1; break;
case 'm': csi = 1; min_shift = atoi(optarg); break;
default:
index_usage(pysamerr);
return 1;
}
if (optind == argc) {
index_usage(stdout);
return 1;
}
if (argc - optind > 1) bam_index_build2(argv[optind], argv[optind+1]);
else bam_index_build(argv[optind], csi? min_shift : 0);
return 0;
}
int bam_index(int argc, char *argv[])
{
int csi = 0;
int min_shift = BAM_LIDX_SHIFT;
int c, ret;
while ((c = getopt(argc, argv, "bcm:")) >= 0)
switch (c) {
case 'b':
csi = 0;
break;
case 'c':
csi = 1;
break;
case 'm':
csi = 1;
min_shift = atoi(optarg);
break;
default:
index_usage(stderr);
return 1;
}
if (optind == argc) {
index_usage(stdout);
return 1;
}
ret = sam_index_build2(argv[optind], argv[optind+1], csi? min_shift : 0);
if (ret != 0) {
fprintf(stderr, "[%s] corrupted or unsorted input file\n", __func__);
return EXIT_FAILURE;
}
return 0;
}
