struct pipeline *pipelineOpenFd(char ***cmds, unsigned opts,
int otherEndFd, int stderrFd)
/* Create a pipeline from an array of commands. See pipeline.h for
* full documentation. */
{
struct pipeline *pl;
checkOpts(opts);
pl = pipelineNew(cmds, opts);
if (opts & pipelineRead)
pipelineStartRead(pl, otherEndFd, stderrFd, NULL, 0);
else
pipelineStartWrite(pl, otherEndFd, stderrFd);
return pl;
}
struct pipeline *pipelineOpenMem(char ***cmds, unsigned opts,
void *otherEndBuf, size_t otherEndBufSize,
int stderrFd)
/* Create a pipeline from an array of commands, with the pipeline input/output
* in a memory buffer. See pipeline.h for full documentation. Currently only
* input to a read pipeline is supported */
{
struct pipeline *pl;
checkOpts(opts);
if (opts & pipelineWrite)
errAbort("pipelineOpenMem only supports read pipelines at this time");
opts |= pipelineMemInput;
pl = pipelineNew(cmds, opts);
pipelineStartRead(pl, STDIN_FILENO, stderrFd, otherEndBuf, otherEndBufSize);
return pl;
}
struct pipeline *pipelineOpen(char ***cmds, unsigned opts,
char *otherEndFile, char *stderrFile)
/* Create a pipeline from an array of commands. See pipeline.h for
* full documentation */
{
int otherEndFd;
int stderrFd = (stderrFile == NULL) ? STDERR_FILENO : openWrite(stderrFile);
checkOpts(opts);
if (opts & pipelineRead)
otherEndFd = (otherEndFile == NULL) ? STDIN_FILENO : openRead(otherEndFile);
else
otherEndFd = (otherEndFile == NULL) ? STDOUT_FILENO : openWrite(otherEndFile);
struct pipeline *pl = pipelineOpenFd(cmds, opts, otherEndFd, stderrFd);
safeClose(&otherEndFd);
if (stderrFile != NULL)
safeClose(&stderrFd);
return pl;
}
void getOpts(int argc, char** argv)
{
int c;
while (1)
{
int option_index = 0;
static struct option long_options[] = {
{"gz1", required_argument, 0, 0 },
{"gz2", required_argument, 0, 0 },
{"output", required_argument, 0, 0 },
{"callId", required_argument, 0, 0 },
{"row", required_argument, 0, 0 },
{"log", required_argument, 0, 0 },
{0, 0, 0, 0 }
};
c = getopt_long(argc, argv, ":c",
long_options, &option_index);
if (c == -1)
{
break;
}
switch (c) {
case 0:
printf("option %s", long_options[option_index].name);
if (optarg)
printf(" with arg %s", optarg);
printf("\n");
if (long_options[option_index].flag != 0) {
cout << "break after flag test! \n";
break;
}
if (strcmp(long_options[option_index].name,"gz1") == 0) {
gz1_path = optarg;
cout << gz1_path << endl;
}
if (strcmp(long_options[option_index].name,"gz2") == 0) {
if(optarg)
{
gz2_path = optarg;
cout << gz2_path << endl;
}
}
if (strcmp(long_options[option_index].name,"output") == 0) {
output_path = optarg;
cout << output_path << endl;
}
if (strcmp(long_options[option_index].name,"row") == 0) {
row_num = atoi(optarg);
cout << row_num << endl;
}
if (strcmp(long_options[option_index].name,"sample") == 0) {
sample_name = optarg;
cout << sample_name << endl;
}
if (strcmp(long_options[option_index].name,"log") == 0) {
log_path = optarg;
cout << log_path << endl;
}
if (strcmp(long_options[option_index].name,"callId") == 0) {
call_id = optarg;
cout << call_id << endl;
}
break;
case 'c':
is_compress = true;
printf("compress the result\n");
break;
default:
printf("?? getopt returned character code 0%o ??\n", c);
}
}
if (optind < argc)
{
printf("non-option ARGV-elements: ");
while (optind < argc)
printf("%s ", argv[optind++]);
printf("\n");
}
// check options
checkOpts(argv);
// init log path
initLogPath();
}
