static int thread_printheader(logbuffer_t * logbuf)
{
logbuf->logsize = 0;
log_header_t header = log_header_INIT("thread_printheader", __FILE__, 100);
printheader_logbuffer(logbuf, &header);
TEST(0 == compare_header(logbuf->logsize, logbuf->addr, "thread_printheader", __FILE__, 100));
return 0;
ONERR:
CLEARBUFFER_ERRLOG();
return EINVAL;
}
static int test_update(void)
{
logbuffer_t logbuf = logbuffer_FREE;
thread_t * thread = 0;
pipe_t pipe = pipe_FREE;
uint8_t buffer[1024];
uint8_t readbuffer[1024+1];
// prepare
TEST(0 == init_pipe(&pipe));
logbuf = (logbuffer_t) logbuffer_INIT(sizeof(buffer), buffer, pipe.write);
// TEST truncate_logbuffer
for (unsigned i = 0; i < 32; ++i) {
logbuf.logsize = 32;
logbuf.addr[i] = 'a';
truncate_logbuffer(&logbuf, i);
TEST(logbuf.addr == buffer);
TEST(logbuf.size == sizeof(buffer));
TEST(logbuf.io == pipe.write);
TEST(logbuf.addr[i] == 0);
TEST(logbuf.logsize == i);
}
// TEST truncate_logbuffer: parameter with bigger or equal size are ignored
for (unsigned i = 0; i < 32; ++i) {
logbuf.logsize = i;
logbuf.addr[i] = 'a';
logbuf.addr[i+1] = 'a';
truncate_logbuffer(&logbuf, i+1);
truncate_logbuffer(&logbuf, i);
TEST(logbuf.addr == buffer);
TEST(logbuf.size == sizeof(buffer));
TEST(logbuf.io == pipe.write);
TEST(logbuf.addr[i] == 'a');
TEST(logbuf.addr[i+1] == 'a');
TEST(logbuf.logsize == i);
}
// TEST write_logbuffer
memset(readbuffer, 0, sizeof(readbuffer));
for (unsigned i = 0; i < sizeof(buffer); ++i) {
buffer[i] = (uint8_t)i;
}
logbuf.logsize = logbuf.size;
// test
TEST( 0 == write_logbuffer(&logbuf));
// check logbuf
TEST( logbuf.addr == buffer);
TEST( logbuf.size == sizeof(buffer));
TEST( logbuf.logsize == sizeof(buffer));
TEST( logbuf.io == pipe.write);
// check content of pipe
static_assert(sizeof(readbuffer) > sizeof(buffer), "check that only sizeof(buffer) are written");
TEST(sizeof(buffer) == read(pipe.read, readbuffer, sizeof(readbuffer)));
for (unsigned i = 0; i < sizeof(buffer); ++i) {
TEST(buffer[i] == readbuffer[i]);
}
// TEST printheader_logbuffer
logbuf.logsize = 0;
log_header_t header = log_header_INIT("test_update", "file", 123456);
printheader_logbuffer(&logbuf, &header);
TEST(0 == compare_header(logbuf.logsize, logbuf.addr, "test_update", "file", 123456));
for (size_t len = logbuf.logsize, i = 1; i < 10; ++i) {
printheader_logbuffer(&logbuf, &header);
TEST((i+1)*len == logbuf.logsize);
TEST(0 == compare_header(len, logbuf.addr + i*len, "test_update", "file", 123456));
}
// TEST printheader_logbuffer: other thread
TEST(0 == newgeneric_thread(&thread, &thread_printheader, &logbuf));
TEST(0 == join_thread(thread));
TEST(0 == returncode_thread(thread));
TEST(0 == delete_thread(&thread));
// TEST printheader_logbuffer: adds " ..." at end in case of truncated message
logbuf.logsize = logbuf.size - 10;
logbuf.addr[logbuf.logsize] = 0;
printheader_logbuffer(&logbuf, &header);
TEST(logbuf.logsize == logbuf.size - 1)
TEST(0 == memcmp(logbuf.addr + logbuf.size - 10, "[", 1));
TEST(0 == memcmp(logbuf.addr + logbuf.size - 5, " ...", 5));
// TEST vprintf_logbuffer: append on already stored content
for (unsigned i = 0; i < sizeof(buffer)-100; ++i) {
memset(buffer, 0, sizeof(buffer));
memset(readbuffer, 0, sizeof(readbuffer));
logbuf.logsize = i;
printf_logbuffer(&logbuf, "%d : %s : %c;;", i, "OK!", '0');
snprintf((char*)readbuffer + i, 100, "%d : %s : %c;;", i, "OK!", '0');
TEST(0 == memcmp(buffer, readbuffer, sizeof(buffer)));
}
// TEST vprintf_logbuffer: different formats
logbuf.logsize = 0;
printf_logbuffer(&logbuf, "%%%s%%", "str" );
printf_logbuffer(&logbuf, "%"PRIi8";", (int8_t)-1);
printf_logbuffer(&logbuf, "%"PRIu8";", (uint8_t)1);
printf_logbuffer(&logbuf, "%"PRIi16";", (int16_t)-256);
printf_logbuffer(&logbuf, "%"PRIu16";", (uint16_t)256);
printf_logbuffer(&logbuf, "%"PRIi32";", (int32_t)-65536);
printf_logbuffer(&logbuf, "%"PRIu32";", (uint32_t)65536);
printf_logbuffer(&logbuf, "%zd;", (ssize_t)-65536);
printf_logbuffer(&logbuf, "%zu;", (size_t)65536);
printf_logbuffer(&logbuf, "%g;", 2e100);
printf_logbuffer(&logbuf, "%.0f;", (double)1234567);
const char * result = "%str%-1;1;-256;256;-65536;65536;-65536;65536;2e+100;1234567;";
TEST(strlen(result) == logbuf.logsize);
TEST(0 == memcmp(logbuf.addr, result, logbuf.logsize));
// TEST vprintf_logwriter: adds " ..." at end in case of truncated message
char strtoobig[100];
memset(strtoobig, '1', sizeof(strtoobig));
logbuf.logsize = logbuf.size - sizeof(strtoobig);
logbuf.addr[logbuf.logsize] = 0;
printf_logbuffer(&logbuf, "%.100s", strtoobig);
TEST(logbuf.logsize == logbuf.size - 1)
TEST(0 == memcmp(logbuf.addr + logbuf.size - sizeof(strtoobig), strtoobig, sizeof(strtoobig)-5));
TEST(0 == memcmp(logbuf.addr + logbuf.size - 5, " ...", 5));
// TEST vprintf_logbuffer: format == 0
logbuf.logsize = 0;
printf_logbuffer(&logbuf, 0);
// nothing printed
TEST(0 == logbuf.logsize);
// TEST vprintf_logbuffer: sizefree_logbuffer() == 0
logbuf.logsize = logbuf.size;
memset(logbuf.addr, 255, logbuf.size);
printf_logbuffer(&logbuf, "%d", 12345);
// check logbuf not changed
TEST(buffer == logbuf.addr);
TEST(sizeof(buffer) == logbuf.size);
TEST(sizeof(buffer) == logbuf.logsize);
TEST(pipe.write == logbuf.io);
// check content of logbuf not changed except for " ..."
for (size_t i = 0; i < logbuf.logsize - 5; ++i) {
TEST(255 == logbuf.addr[i]);
}
TEST(0 == memcmp(logbuf.addr + logbuf.logsize - 5, " ...", 4));
TEST(255 == logbuf.addr[logbuf.logsize-1]);
// TEST vprintf_logbuffer: logbuffer_t.size <= 5
for (size_t s = 5; s <= 5; --s) {
TEST(sizeof(buffer) == logbuf.size);
logbuf.size = s;
logbuf.logsize = 0;
memset(logbuf.addr, 255, s);
printf_logbuffer(&logbuf, "%d", 12345);
// check logbuf
TEST(buffer == logbuf.addr);
TEST(s == logbuf.size);
TEST((s?s-1:0) == logbuf.logsize);
TEST(pipe.write == logbuf.io);
// check content of logbuf
if (s == 5) {
// " ..."
TEST(0 == memcmp(logbuf.addr, " ...", 5));
} else {
// truncated 12345
for (size_t i = 0; i < logbuf.logsize; ++i) {
TEST(i+'1' == logbuf.addr[i]);
}
TEST(0 == (logbuf.size ? logbuf.addr[logbuf.size-1] : 0));
}
// reset
logbuf.size = sizeof(buffer);
}
// unprepare
TEST(-1 == read(pipe.read, readbuffer, sizeof(readbuffer)));
TEST(0 == free_pipe(&pipe));
return 0;
ONERR:
delete_thread(&thread);
free_pipe(&pipe);
return EINVAL;
}
int main_vcfquery(int argc, char *argv[])
{
int c, collapse = 0;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"list-samples",0,0,'l'},
{"include",1,0,'i'},
{"exclude",1,0,'e'},
{"format",1,0,'f'},
{"output-file",1,0,'o'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"annots",1,0,'a'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"print-header",0,0,'H'},
{"collapse",1,0,'c'},
{"vcf-list",1,0,'v'},
{"allow-undef-tags",0,0,'u'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
switch (c) {
case 'o': args->fn_out = optarg; break;
case 'f': args->format_str = strdup(optarg); break;
case 'H': args->print_header = 1; break;
case 'v': args->vcf_list = optarg; break;
case 'c':
if ( !strcmp(optarg,"snps") ) collapse |= COLLAPSE_SNPS;
else if ( !strcmp(optarg,"indels") ) collapse |= COLLAPSE_INDELS;
else if ( !strcmp(optarg,"both") ) collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
else if ( !strcmp(optarg,"any") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"all") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"some") ) collapse |= COLLAPSE_SOME;
else error("The --collapse string \"%s\" not recognised.\n", optarg);
break;
case 'a':
{
kstring_t str = {0,0,0};
kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str);
char *p = optarg;
while ( *p )
{
if ( *p==',' )
kputs("\t%", &str);
else
kputc(*p, &str);
p++;
}
kputc('\n', &str);
args->format_str = str.s;
break;
}
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'l': args->list_columns = 1; break;
case 'u': args->allow_undef_tags = 1; break;
case 's': args->sample_list = optarg; break;
case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
char *fname = NULL;
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
}
else fname = argv[optind];
if ( args->list_columns )
{
if ( !fname ) error("Missing the VCF file name\n");
args->files = bcf_sr_init();
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
list_columns(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
if ( !args->format_str ) usage();
args->out = args->fn_out ? fopen(args->fn_out, "w") : stdout;
if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
if ( !args->vcf_list )
{
if ( !fname ) usage();
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( optind+1 < argc ) args->files->require_index = 1;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
while ( fname )
{
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
fname = ++optind < argc ? argv[optind] : NULL;
}
init_data(args);
query_vcf(args);
free(args->format_str);
destroy_data(args);
bcf_sr_destroy(args->files);
fclose(args->out);
free(args);
return 0;
}
// multiple VCFs
int i, k, nfiles, prev_nsamples = 0;
char **fnames, **prev_samples = NULL;
fnames = hts_readlist(args->vcf_list, 1, &nfiles);
if ( !nfiles ) error("No files in %s?\n", args->vcf_list);
for (i=0; i<nfiles; i++)
{
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( optind < argc ) args->files->require_index = 1;
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum));
for (k=optind; k<argc; k++)
if ( !bcf_sr_add_reader(args->files, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum));
init_data(args);
if ( i==0 )
prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header));
else
{
args->print_header = 0;
if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) )
error("Different samples in %s and %s\n", fnames[i-1],fnames[i]);
}
query_vcf(args);
destroy_data(args);
bcf_sr_destroy(args->files);
}
fclose(args->out);
destroy_list(fnames, nfiles);
destroy_list(prev_samples, prev_nsamples);
free(args->format_str);
free(args);
return 0;
}