plugin_min_phred.c

#include<stdlib.h>
#include<pandaseq-plugin.h>

HELP("Ensure the minimum score of all the output bases is above a certain PHRED value.", "min_phred:value");

VER_INFO("1.0");

static bool check_func(
	PandaLogProxy logger,
	const panda_result_seq *sequence,
	void *user_data) {
	size_t it;

	(void) logger;

	for (it = 0; it < sequence->sequence_length; it++) {
		if (panda_result_phred(&sequence->sequence[it]) < *(int *) user_data) {
			return false;
		}
	}
	return true;
}

OPEN {
	long int value;
	char *endptr;

	(void) precheck;

	if (args == NULL || *args == '\0') {
		panda_log_proxy_write_str(logger, "Need a number for a PHRED score.\n");
		return false;
	}

	value = strtol(args, &endptr, 10);
	if ((endptr != NULL && *endptr != '\0') || value < 0 || value > 127) {
		panda_log_proxy_write_str(logger, "PHRED score must be a number between 0 and 127.\n");
		return false;
	}
	*check = check_func;
	*user_data = PANDA_STRUCT_DUP(&value);
	*destroy = free;
	return true;
}