void test() {
int fd;
#if FIRST
// for each file, we first make sure it doesn't currently exist
// (we delete it at the end of !FIRST). We then test an empty
// file plus two files each with a small amount of content
struct stat st;
// the empty file
if ((stat("/working1/empty.txt", &st) != -1) || (errno != ENOENT))
result = -1000 - errno;
fd = open("/working1/empty.txt", O_RDWR | O_CREAT, 0666);
if (fd == -1)
result = -2000 - errno;
else if (close(fd) != 0)
result = -3000 - errno;
// a file whose contents are just 'az'
if ((stat("/working1/waka.txt", &st) != -1) || (errno != ENOENT))
result = -4000 - errno;
fd = open("/working1/waka.txt", O_RDWR | O_CREAT, 0666);
if (fd == -1)
result = -5000 - errno;
else
{
if (write(fd,"az",2) != 2)
result = -6000 - errno;
if (close(fd) != 0)
result = -7000 - errno;
}
// a file whose contents are random-ish string set by the test_browser.py file
if ((stat("/working1/moar.txt", &st) != -1) || (errno != ENOENT))
result = -8000 - errno;
fd = open("/working1/moar.txt", O_RDWR | O_CREAT, 0666);
if (fd == -1)
result = -9000 - errno;
else
{
if (write(fd, SECRET, strlen(SECRET)) != strlen(SECRET))
result = -10000 - errno;
if (close(fd) != 0)
result = -11000 - errno;
}
#else
// does the empty file exist?
fd = open("/working1/empty.txt", O_RDONLY);
if (fd == -1)
result = -12000 - errno;
else if (close(fd) != 0)
result = -13000 - errno;
if (unlink("/working1/empty.txt") != 0)
result = -14000 - errno;
// does the 'az' file exist, and does it contain 'az'?
fd = open("/working1/waka.txt", O_RDONLY);
if (fd == -1)
result = -15000 - errno;
else
{
char bf[4];
int bytes_read = read(fd,&bf[0],sizeof(bf));
if (bytes_read != 2)
result = -16000;
else if ((bf[0] != 'a') || (bf[1] != 'z'))
result = -17000;
if (close(fd) != 0)
result = -18000 - errno;
if (unlink("/working1/waka.txt") != 0)
result = -19000 - errno;
}
// does the random-ish file exist and does it contain SECRET?
fd = open("/working1/moar.txt", O_RDONLY);
if (fd == -1)
result = -20000 - errno;
else
{
char bf[256];
int bytes_read = read(fd,&bf[0],sizeof(bf));
if (bytes_read != strlen(SECRET))
result = -21000;
else
{
bf[strlen(SECRET)] = 0;
if (strcmp(bf,SECRET) != 0)
result = -22000;
}
if (close(fd) != 0)
result = -23000 - errno;
if (unlink("/working1/moar.txt") != 0)
result = -24000 - errno;
}
#endif
// sync from memory state to persisted and then
// run 'success'
EM_ASM(
FS.syncfs(function (err) {
assert(!err);
ccall('success', 'v');
});
int main_vcfcall(int argc, char *argv[])
{
char *ploidy_fname = NULL, *ploidy = NULL;
args_t args;
memset(&args, 0, sizeof(args_t));
args.argc = argc; args.argv = argv;
args.aux.prior_type = -1;
args.aux.indel_frac = -1;
args.aux.theta = 1.1e-3;
args.aux.pref = 0.5;
args.aux.min_perm_p = 0.01;
args.aux.min_lrt = 1;
args.flag = CF_ACGT_ONLY;
args.output_fname = "-";
args.output_type = FT_VCF;
args.aux.trio_Pm_SNPs = 1 - 1e-8;
args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9;
int c;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"gvcf",1,0,'g'},
{"format-fields",1,0,'f'},
{"output",1,0,'o'},
{"output-type",1,0,'O'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"keep-alts",0,0,'A'},
{"insert-missed",0,0,'i'},
{"skip-Ns",0,0,'N'}, // now the new default
{"keep-masked-refs",0,0,'M'},
{"skip-variants",1,0,'V'},
{"variants-only",0,0,'v'},
{"consensus-caller",0,0,'c'},
{"constrain",1,0,'C'},
{"multiallelic-caller",0,0,'m'},
{"pval-threshold",1,0,'p'},
{"prior",1,0,'P'},
{"chromosome-X",0,0,'X'},
{"chromosome-Y",0,0,'Y'},
{"novel-rate",1,0,'n'},
{"ploidy",1,0,1},
{"ploidy-file",1,0,2},
{0,0,0,0}
};
char *tmp = NULL;
while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:XYn:P:f:ig:", loptions, NULL)) >= 0)
{
switch (c)
{
case 'g':
args.flag |= CF_GVCF;
args.gvcf.min_dp = strtol(optarg,&tmp,10);
if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
break;
case 2 : ploidy_fname = optarg; break;
case 1 : ploidy = optarg; break;
case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
case 'f': args.aux.output_tags |= parse_format_flag(optarg); break;
case 'M': args.flag &= ~CF_ACGT_ONLY; break; // keep sites where REF is N
case 'N': args.flag |= CF_ACGT_ONLY; break; // omit sites where first base in REF is N (the new default)
case 'A': args.aux.flag |= CALL_KEEPALT; break;
case 'c': args.flag |= CF_CCALL; break; // the original EM based calling method
case 'i': args.flag |= CF_INS_MISSED; break;
case 'v': args.aux.flag |= CALL_VARONLY; break;
case 'o': args.output_fname = optarg; break;
case 'O':
switch (optarg[0]) {
case 'b': args.output_type = FT_BCF_GZ; break;
case 'u': args.output_type = FT_BCF; break;
case 'z': args.output_type = FT_VCF_GZ; break;
case 'v': args.output_type = FT_VCF; break;
default: error("The output type \"%s\" not recognised\n", optarg);
}
break;
case 'C':
if ( !strcasecmp(optarg,"alleles") ) args.aux.flag |= CALL_CONSTR_ALLELES;
else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
else error("Unknown argument to -C: \"%s\"\n", optarg);
break;
case 'V':
if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
else error("Unknown skip category \"%s\" (-S argument must be \"snps\" or \"indels\")\n", optarg);
break;
case 'm': args.flag |= CF_MCALL; break; // multiallelic calling method
case 'p':
args.aux.pref = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse: --pval-threshold %s\n", optarg);
break;
case 'P': args.aux.theta = strtod(optarg,&tmp);
if ( *tmp ) error("Could not parse, expected float argument: -P %s\n", optarg);
break;
case 'n': parse_novel_rate(&args,optarg); break;
case 'r': args.regions = optarg; break;
case 'R': args.regions = optarg; args.regions_is_file = 1; break;
case 't': args.targets = optarg; break;
case 'T': args.targets = optarg; args.targets_is_file = 1; break;
case 's': args.samples_fname = optarg; break;
case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
default: usage(&args);
}
}
// Sanity check options and initialize
if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-"; // reading from stdin
else usage(&args);
}
else args.bcf_fname = argv[optind++];
if ( !ploidy_fname && !ploidy )
{
fprintf(stderr,"Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid\n");
args.ploidy = ploidy_init_string("",2);
}
if ( !args.ploidy ) error("Could not initialize ploidy\n");
if ( args.flag & CF_GVCF )
{
// Force some flags to avoid unnecessary branching
args.aux.flag &= ~CALL_KEEPALT;
args.aux.flag |= CALL_VARONLY;
}
if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n"); // not sure about this, please fix
if ( args.aux.flag & CALL_CONSTR_ALLELES )
{
if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
}
if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
init_data(&args);
while ( bcf_sr_next_line(args.aux.srs) )
{
bcf1_t *bcf_rec = args.aux.srs->readers[0].buffer[0];
if ( args.samples_map ) bcf_subset(args.aux.hdr, bcf_rec, args.nsamples, args.samples_map);
bcf_unpack(bcf_rec, BCF_UN_STR);
// Skip unwanted sites
if ( args.aux.flag & CALL_VARONLY )
{
int is_ref = 0;
if ( bcf_rec->n_allele==1 ) is_ref = 1; // not a variant
else if ( bcf_rec->n_allele==2 )
{
// second allele is mpileup's X, not a variant
if ( bcf_rec->d.allele[1][0]=='X' ) is_ref = 1;
else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='X' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='*' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
}
if ( is_ref )
{
// gVCF output
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, 1);
continue;
}
}
if ( (args.flag & CF_INDEL_ONLY) && bcf_is_snp(bcf_rec) ) continue; // not an indel
if ( (args.flag & CF_NO_INDEL) && !bcf_is_snp(bcf_rec) ) continue; // not a SNP
if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue; // REF[0] is 'N'
bcf_unpack(bcf_rec, BCF_UN_ALL);
if ( args.nsex ) set_ploidy(&args, bcf_rec);
// Various output modes: QCall output (todo)
if ( args.flag & CF_QCALL )
{
qcall(&args.aux, bcf_rec);
continue;
}
// Calling modes which output VCFs
int ret;
if ( args.flag & CF_MCALL )
ret = mcall(&args.aux, bcf_rec);
else
ret = ccall(&args.aux, bcf_rec);
if ( ret==-1 ) error("Something is wrong\n");
// gVCF output
if ( args.flag & CF_GVCF )
{
gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, ret?0:1);
continue;
}
// Normal output
if ( (args.aux.flag & CALL_VARONLY) && ret==0 ) continue; // not a variant
bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
}
if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, NULL, 0);
if ( args.flag & CF_INS_MISSED ) bcf_sr_regions_flush(args.aux.srs->targets);
destroy_data(&args);
return 0;
}
