/**
Composes the name of an input file, based on target
Takes a data directory and an executable name, and tries to open an input
file based on these variables. If a file is found in neither of two
locattions derived from these variables, this method tries to fall back on
/dev/null.
Source file locations:
- [data_dir]/manual/in/[target].in
- [data_dir]/tutorial/in/[target].in
- /dev/null
@param data_dir the path of the reference data directory
@param target the name of executable being run
@returns the name of the file
*/
char*
input_name (const char* data_dir, const char* target)
{
char* fname = 0;
int stat_result = 0;
struct stat sb;
assert (0 != target);
if (data_dir && *data_dir) {
/* Try data_dir/manual/in/target.in */
fname = reference_name (data_dir, "manual", "in");
stat_result = stat (fname, &sb);
if (0 == stat_result)
return fname;
free (fname);
/* Try data_dir/tutorial/in/target.in */
fname = reference_name (data_dir, "tutorial", "in");
stat_result = stat (fname, &sb);
if (0 == stat_result)
return fname;
free (fname);
}
/* If we didn't find a source file, use /dev/null */
fname = (char*)RW_MALLOC (sizeof DEV_NULL);
strcpy (fname, DEV_NULL);
return fname;
}
std::string record_to_string(const bam_hdr_t* header, const bam1_t* record) {
std::string reference_name(record->core.tid >= 0 ? header->target_name[record->core.tid] : "*");
std::string mate_reference_name(record->core.mtid >= 0 ? header->target_name[record->core.mtid] : "*");
std::stringstream s;
s << get_qname(record)
<< "\t" << record->core.flag
<< "\t" << reference_name
<< "\t" << record->core.pos + 1
<< "\t" << mate_reference_name
<< "\t" << record->core.mpos + 1
<< "\t" << record->core.isize;
return s.str();
}
/**
Parses output file out_name for the example target_name.
This method tries to compare out_name against a reference output file and
reports the result of the comparison. If the comparison fails to result in
a match, status->status is set to the appropriate error state. The
reference file name is generated by the reference_name function.
Reference file locations:
- [data_dir]/manual/out/[target_name].out
- [data_dir]/tutorial/out/[target_name].out
@todo add logic to handle differing line endings (CR vs LF vs CRLF)
@param out_name the name of the output file
@param fout pointer to file structure for output file being parsed
@param status status object to record results in.
@see reference_name
*/
static void
check_example (const char* const data_dir, char* const out_name, FILE* fout,
struct target_status* status)
{
struct stat file_info;
char* ref_name;
FILE* fref; /* reference file (expected output) */
assert (0 != out_name);
assert (0 != fout);
assert (0 != status);
/* Mark as an example by setting assertions to -1 */
status->assert = (unsigned)-1;
/* Try data_dir/manual/out/target_name.out */
ref_name = reference_name (data_dir, "manual", "out");
if (0 > stat (ref_name, &file_info)) {
if (ENOENT != errno) {
warn ("stat (%s) error: %s\n", exe_name, ref_name,
strerror (errno));
status->status = ST_BAD_REF;
free (ref_name);
return;
}
/* If that doesn't exist, try
data_dir/tutorial/out/target_name.out */
free (ref_name);
ref_name = reference_name (data_dir, "tutorial", "out");
if (0 > stat (ref_name, &file_info)) {
if (ENOENT != errno) {
warn ("stat (%s) error: %s\n", exe_name, ref_name,
strerror (errno));
status->status = ST_BAD_REF;
}
else
status->status = ST_NO_REF;
free (ref_name);
return;
}
}
fref = fopen (ref_name, "r");
if (0 == fref) {
int cache = errno; /* caching errno, as puts could alter it */
if (ENOENT != cache)
warn ("Error opening %s: %s\n", ref_name, strerror (cache));
status->status = ST_BAD_REF;
}
else {
int match = 1; /* do the two files match? */
while (!feof (fref) && !feof (fout)) {
char buf [2][DELTA_BUF_LEN];
size_t nread [2]; /* bytes read from the output/ref file */
/* First, read a block from the files into the buffer */
nread [0] = fread (buf [0], 1, sizeof buf [0], fout);
if (ferror (fout)) {
warn ("Error reading %s: %s\n", out_name, strerror (errno));
match = 0;
break;
}
nread [1] = fread (buf [1], 1, sizeof buf [1], fref);
if (ferror (fref)) {
warn ("Error reading %s: %s\n", ref_name, strerror (errno));
match = 0;
break;
}
/* Then, check if the amount of data read or the state of the
files differs
*/
if (nread [0] != nread [1] || feof (fref) != feof (fout)) {
match = 0;
break;
}
/* Finally, check if the contents of the buffers differ */
if (0 != memcmp (buf [0], buf [1], nread [0])) {
match = 0;
break;
}
}
if (!match)
status->status = ST_BAD_OUTPUT;
fclose (fref);
}
free (ref_name);
}
