void printCounts(char *chr,int *posi,suint **counts,int nSites,size_t nInd,kstring_t &bpos,kstring_t &bbin,int dumpType,int *keepSites){
bpos.l=bbin.l=0;
for(int s=0;s<nSites;s++){
if(keepSites[s]==0)
continue;
ksprintf(&bpos, "%s\t%d\t%d\n",chr,posi[s]+1,calcSum(counts[s],4*nInd));
//if we need per sample info
if(dumpType>1) {
if(dumpType==4)//count A,C,G,T
for(int i=0;i<4*nInd;i++)
ksprintf(&bbin,"%u\t",counts[s][i]);
else if(dumpType==2){//print A+C+G+T
for(int n=0;n<nInd;n++)
ksprintf(&bbin,"%u\t",counts[s][n*4]+counts[s][n*4+1]+counts[s][n*4+2]+counts[s][n*4+3]);
}else{//overall sum of A,C,G,T
size_t tsum[4]={0,0,0,0};
for(int i=0;i<4*nInd;i++)
tsum[i%4] +=counts[s][i];
ksprintf(&bbin,"%zu\t%zu\t%zu\t%zu",tsum[0],tsum[1],tsum[2],tsum[3]);
}
kputc('\n',&bbin);
}
}
}
bam_header_t *sam_header_read2(const char *fn)
{
bam_header_t *header;
int c, dret, n_targets = 0;
gzFile fp;
kstream_t *ks;
kstring_t *str;
kstring_t samstr = { 0, 0, NULL };
if (fn == 0) return 0;
fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
if (fp == 0) return 0;
ks = ks_init(fp);
str = (kstring_t*)calloc(1, sizeof(kstring_t));
while (ks_getuntil(ks, 0, str, &dret) > 0) {
ksprintf(&samstr, "@SQ\tSN:%s", str->s);
ks_getuntil(ks, 0, str, &dret);
ksprintf(&samstr, "\tLN:%d\n", atoi(str->s));
n_targets++;
if (dret != '\n')
while ((c = ks_getc(ks)) != '\n' && c != -1);
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
header = sam_hdr_parse(samstr.l, samstr.s? samstr.s : "");
free(samstr.s);
fprintf(pysamerr, "[sam_header_read2] %d sequences loaded.\n", n_targets);
return header;
}
static void
afd_describe(device_t dev)
{
struct ata_channel *ch = device_get_softc(device_get_parent(dev));
struct ata_device *atadev = device_get_softc(dev);
struct afd_softc *fdp = device_get_ivars(dev);
char sizestring[16];
if (fdp->mediasize > 1048576 * 5)
ksprintf(sizestring, "%lluMB", (unsigned long long)
(fdp->mediasize / 1048576));
else if (fdp->mediasize)
ksprintf(sizestring, "%lluKB", (unsigned long long)
(fdp->mediasize / 1024));
else
strcpy(sizestring, "(no media)");
device_printf(dev, "%s <%.40s %.8s> at ata%d-%s %s\n",
sizestring, atadev->param.model, atadev->param.revision,
device_get_unit(ch->dev),
(atadev->unit == ATA_MASTER) ? "master" : "slave",
ata_mode2str(atadev->mode));
if (bootverbose) {
device_printf(dev, "%llu sectors [%lluC/%dH/%dS]\n",
(unsigned long long)(fdp->mediasize / fdp->sectorsize),
(unsigned long long)
(fdp->mediasize/(fdp->sectorsize*fdp->sectors*fdp->heads)),
fdp->heads, fdp->sectors);
}
}
/*
* Executes hash_dmp_fn on each of the temporary files in the splitterhash
* and cleans up if not disabled.
*/
void parallel_hash_dmp_core(marksplit_settings_t *settings, splitterhash_params_t *params, hash_dmp_fn func)
{
#pragma omp parallel for schedule(dynamic, 1)
for(int i = 0; i < settings->n_handles; ++i) {
LOG_DEBUG("Now running hash dmp core on input filename %s and output filename %s.\n",
params->infnames_r1[i], params->outfnames_r1[i]);
func(params->infnames_r1[i], params->outfnames_r1[i], settings->gzip_compression);
if(settings->cleanup) {
kstring_t ks{0, 0, nullptr};
ksprintf(&ks, "rm %s", params->infnames_r1[i]);
dlib::check_call(ks.s);
free(ks.s);
}
}
if(settings->is_se) {
LOG_DEBUG("Only dmp'ing single end.\n");
return; // Don't dmp imaginary files....
}
#pragma omp parallel for schedule(dynamic, 1)
for(int i = 0; i < settings->n_handles; ++i) {
LOG_DEBUG("Now running hash dmp core on input filename %s and output filename %s.\n",
params->infnames_r2[i], params->outfnames_r2[i]);
func(params->infnames_r2[i], params->outfnames_r2[i], settings->gzip_compression);
if(settings->cleanup) {
kstring_t ks{0, 0, nullptr};
ksprintf(&ks, "rm %s", params->infnames_r2[i]);
dlib::check_call(ks.s);
free(ks.s);
}
}
}
void cat_fastqs_pe(marksplit_settings_t *settings, splitterhash_params_t *params, char *ffq_r1, char *ffq_r2)
{
kstring_t ks1{0, 0, nullptr};
kputsnl("> ", &ks1), kputs(ffq_r1, &ks1);
if(settings->gzip_output) kputsnl(".gz", &ks1);
// Clear output files.
//ksprintf(&ks1, settings->gzip_output ? "> %s.gz" : "> %s", ffq_r1);
dlib::check_call(ks1.s); ks1.l = 0;
ksprintf(&ks1, settings->gzip_output ? "> %s.gz" : "> %s", ffq_r2);
dlib::check_call(ks1.s); ks1.l = 0;
kputsnl("/bin/cat ", &ks1);
kstring_t ks2{0};
kputsn(ks1.s, ks1.l, &ks2);
for(int i(0); i < settings->n_handles; ++i) {
if(!dlib::isfile(params->outfnames_r1[i]))
LOG_EXIT("Output filename is not a file. Abort! ('%s').\n", params->outfnames_r1[i]);
if(!dlib::isfile(params->outfnames_r2[i]))
LOG_EXIT("Output filename is not a file. Abort! ('%s').\n", params->outfnames_r2[i]);
ksprintf(&ks1, "%s ", params->outfnames_r1[i]);
ksprintf(&ks2, "%s ", params->outfnames_r2[i]);
}
ksprintf(&ks1, " > %s", ffq_r1);
ksprintf(&ks2, " > %s", ffq_r2);
if(settings->gzip_output) {
kputsnl(".gz", &ks1);
kputsnl(".gz", &ks2);
}
FILE *c1_popen(popen(ks1.s, "w"));
FILE *c2_popen(popen(ks2.s, "w"));
int ret;
if((ret = ((pclose(c2_popen) << 8) | pclose(c1_popen)))) {
LOG_EXIT("Background cat command(s) failed. (Code: %i, '%s' or %i, '%s').\n", ret >> 8, ks1.s, ret & 0xff, ks2.s);
}
int main(int argc, char *argv[])
{
extern char *bwa_pg;
int i, ret;
double t_real;
kstring_t pg = {0,0,0};
t_real = realtime();
ksprintf(&pg, "@PG\tID:biscuit\tPN:biscuit\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
bwa_pg = pg.s;
if (argc < 2) return usage();
if (strcmp(argv[1], "index") == 0) ret = main_biscuit_index(argc-1, argv+1);
else if (strcmp(argv[1], "align") == 0) ret = main_align(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) ret = main_pileup(argc-1, argv+1);
else if (strcmp(argv[1], "somatic") == 0) ret = main_somatic(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
err_fflush(stdout);
err_fclose(stdout);
if (ret == 0) {
fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
fprintf(stderr, "[%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
}
free(bwa_pg);
return ret;
}
void
usbd_devinfo(usbd_device_handle dev, int showclass, char *cp)
{
usb_device_descriptor_t *udd = &dev->ddesc;
usbd_interface_handle iface;
char vendor[USB_MAX_STRING_LEN];
char product[USB_MAX_STRING_LEN];
int bcdDevice, bcdUSB;
usb_interface_descriptor_t *id;
usbd_devinfo_vp(dev, vendor, product, 1);
cp += ksprintf(cp, "%s %s", vendor, product);
if (showclass & USBD_SHOW_DEVICE_CLASS)
cp += ksprintf(cp, ", class %d/%d",
udd->bDeviceClass, udd->bDeviceSubClass);
bcdUSB = UGETW(udd->bcdUSB);
bcdDevice = UGETW(udd->bcdDevice);
cp += ksprintf(cp, ", rev ");
cp += usbd_printBCD(cp, bcdUSB);
*cp++ = '/';
cp += usbd_printBCD(cp, bcdDevice);
cp += ksprintf(cp, ", addr %d", dev->address);
if (showclass & USBD_SHOW_INTERFACE_CLASS)
{
/* fetch the interface handle for the first interface */
(void)usbd_device2interface_handle(dev, 0, &iface);
id = usbd_get_interface_descriptor(iface);
cp += ksprintf(cp, ", iclass %d/%d",
id->bInterfaceClass, id->bInterfaceSubClass);
}
*cp = 0;
}
bool addUser::checkMailBox() {
QString mailboxpath;
QString tmp;
struct stat s;
int r;
ksprintf(&mailboxpath, "%s/%s", MAIL_SPOOL_DIR,
(const char *)user->getName());
r = stat(mailboxpath, &s);
if ((r == -1) && (errno == ENOENT))
return true;
if (r == 0)
if (S_ISREG(s.st_mode))
ksprintf(&tmp, i18n("Mailbox %s already exist (uid=%d)"),
(const char *)mailboxpath, s.st_uid);
else
ksprintf(&tmp, i18n("%s exists but is not a regular file"),
(const char *)mailboxpath);
else
ksprintf(&tmp, "checkMail: stat: %s ", strerror(errno));
err->addMsg(tmp, STOP);
err->display();
return false;
}
char *bwa_cal_md1(int n_cigar, jigsaw_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
bwtint_t l_pac, const ubyte_t *pacseq, kstring_t *str, int *_nm)
{
bwtint_t x, y;
int z, u, c, nm = 0;
str->l = 0; // reset
x = pos; y = 0;
if (cigar) {
int k, l;
for (k = u = 0; k < n_cigar; ++k) {
l = __cigar_len(cigar[k]);
uint8_t op = __cigar_op(cigar[k]);
if (op == CIGAR_OP_M) {
for (z = 0; z < l && x+z < l_pac; ++z) {
c = get_pacseq_base (pacseq, x+z);
//c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {//mismatch
ksprintf(str, "%d", u);
kputc("ACGTN"[c], str);
++nm;
u = 0;
} else ++u;
}
x += l; y += l;
/* } else if (cigar[k]>>14 == FROM_I || cigar[k]>>14 == 3) { */
} else if (op == CIGAR_OP_I || op == CIGAR_OP_S) {
y += l;
if (op == FROM_I) nm += l;
} else if (op == CIGAR_OP_D) {
ksprintf(str, "%d", u);
kputc('^', str);
for (z = 0; z < l && x+z < l_pac; ++z)
kputc("ACGT"[get_pacseq_base (pacseq, x+z)], str);
//kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
u = 0;
x += l; nm += l;
} else if (op == CIGAR_OP_N) { //intron
ksprintf(str, "%d", u);
kputc(',', str);
u = 0;
x += l;
}
}
} else { // no gaps
for (z = u = 0; z < len; ++z) {
c = get_pacseq_base (pacseq, x+z);
//c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
ksprintf(str, "%d", u);
kputc("ACGTN"[c], str);
++nm;
u = 0;
} else ++u;
}
}
ksprintf(str, "%d", u);
*_nm = nm;
return strdup(str->s);
}
void bcf_hdr_fmt_text(bcf_hdr_t *hdr)
{
int i,j;
kstring_t txt = {0,0,0};
for (i=0; i<hdr->nhrec; i++)
{
if ( !hdr->hrec[i]->value )
{
ksprintf(&txt, "##%s=<", hdr->hrec[i]->key);
ksprintf(&txt,"%s=%s", hdr->hrec[i]->keys[0], hdr->hrec[i]->vals[0]);
for (j=1; j<hdr->hrec[i]->nkeys; j++)
ksprintf(&txt,",%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]);
ksprintf(&txt,">\n");
}
else
ksprintf(&txt,"##%s=%s\n", hdr->hrec[i]->key,hdr->hrec[i]->value);
}
ksprintf(&txt,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");
if ( hdr->n[BCF_DT_SAMPLE] )
{
ksprintf(&txt,"\tFORMAT");
for (i=0; i<hdr->n[BCF_DT_SAMPLE]; i++)
ksprintf(&txt,"\t%s", hdr->samples[i]);
}
ksprintf(&txt,"\n");
if ( hdr->text ) free(hdr->text);
hdr->text = txt.s;
hdr->l_text = txt.l;
}
static int auth_header_callback(void *ctx, char ***hdrs) {
s3_auth_data *ad = (s3_auth_data *) ctx;
time_t now = time(NULL);
#ifdef HAVE_GMTIME_R
struct tm tm_buffer;
struct tm *tm = gmtime_r(&now, &tm_buffer);
#else
struct tm *tm = gmtime(&now);
#endif
kstring_t message = { 0, 0, NULL };
unsigned char digest[DIGEST_BUFSIZ];
size_t digest_len;
if (!hdrs) { // Closing connection
free_auth_data(ad);
return 0;
}
if (now - ad->auth_time < AUTH_LIFETIME) {
// Last auth string should still be valid
*hdrs = NULL;
return 0;
}
strftime(ad->date, sizeof(ad->date), "Date: %a, %d %b %Y %H:%M:%S GMT", tm);
if (!ad->id.l || !ad->secret.l) {
ad->auth_time = now;
return copy_auth_headers(ad, hdrs);
}
if (ksprintf(&message, "%s\n\n\n%s\n%s%s%s/%s",
ad->mode == 'r' ? "GET" : "PUT", ad->date + 6,
ad->token.l ? "x-amz-security-token:" : "",
ad->token.l ? ad->token.s : "",
ad->token.l ? "\n" : "",
ad->bucket) < 0) {
return -1;
}
digest_len = s3_sign(digest, &ad->secret, &message);
ad->auth_hdr.l = 0;
if (ksprintf(&ad->auth_hdr, "Authorization: AWS %s:", ad->id.s) < 0)
goto fail;
base64_kput(digest, digest_len, &ad->auth_hdr);
free(message.s);
ad->auth_time = now;
return copy_auth_headers(ad, hdrs);
fail:
free(message.s);
return -1;
}
int makeold(int argc,char **argv){
if(argc<1){
fprintf(stderr,"\t-> output is a vcf2fq style file \n");
return 0;
}
args *pars = getArgs(argc,argv);
writepsmc_header(stderr,pars->perc);
double *gls = new double[2*pars->perc->nSites];
size_t at=0;
//first pull all the data
for(myMap::iterator it=pars->perc->mm.begin();it!=pars->perc->mm.end();++it){
if(pars->chooseChr!=NULL)
it = iter_init(pars->perc,pars->chooseChr,pars->start,pars->stop);
else
it = iter_init(pars->perc,it->first,pars->start,pars->stop);
// fprintf(stderr,"it->first:%s\tlast:%lu\n",it->first,pars->perc->last);
memcpy(gls+at,pars->perc->gls,sizeof(double)*2*pars->perc->last);
at += pars->perc->last;
if(pars->chooseChr!=NULL)
break;
}
double opt = 0.01;
double llh = em(opt,gls,at,1e-8);
fprintf(stderr,"estimated het:%f with llh:%f\n",opt,llh);
delete [] gls;
kstring_t kstr;kstr.l=kstr.m=0;kstr.s=NULL;
for(myMap::iterator it=pars->perc->mm.begin();it!=pars->perc->mm.end();++it){
if(pars->chooseChr!=NULL)
it = iter_init(pars->perc,pars->chooseChr,pars->start,pars->stop);
else
it = iter_init(pars->perc,it->first,pars->start,pars->stop);
ksprintf(&kstr,">%s\n",it->first);
double *pp = new double[pars->perc->last];
calcpost(opt,pars->perc->gls,pars->perc->last,pp);
writefa(&kstr,pp,pars->perc->last,100,50,0.9);
if(kstr.l>0&&kstr.s[kstr.l-1]!='\n')
ksprintf(&kstr,"\n");
fwrite(kstr.s,sizeof(char),kstr.l,stdout);
kstr.l=0;
delete [] pp;
if(pars->chooseChr!=NULL)
break;
}
free(kstr.s);
/*
break;
*/
return 0;
}
void frequency::prepPrint(funkyPars *pars){
kstring_t *bufstr = new kstring_t ;
bufstr->s=NULL; bufstr->l=bufstr->m=0;
for(int s=0;s<pars->numSites;s++) {
if(pars->keepSites[s]==0)
continue;
//plugin chr,pos,major,minor
kputs(header->name[pars->refId],bufstr);kputc('\t',bufstr);
kputw(pars->posi[s]+1,bufstr);kputc('\t',bufstr);
kputc(intToRef[pars->major[s]],bufstr);kputc('\t',bufstr);
kputc(intToRef[pars->minor[s]],bufstr);kputc('\t',bufstr);
//plugin ref, anc if exists
if(pars->ref!=NULL)
{kputc(intToRef[pars->ref[s]],bufstr);kputc('\t',bufstr);}
if(pars->anc!=NULL)
{kputc(intToRef[pars->anc[s]],bufstr);kputc('\t',bufstr);}
if(doMaf &1)
ksprintf(bufstr,"%f\t",pars->results->freq->pml[s]);
if(doMaf &2)
ksprintf(bufstr,"%f\t",pars->results->freq->pEM[s]);
if(doMaf &4)
ksprintf(bufstr,"%f\t",pars->results->freq->pmlun[s]);
if(doMaf &8)
ksprintf(bufstr,"%f\t",pars->results->freq->pEMun[s]);
if(doMaf &16)
ksprintf(bufstr,"%f\t",pars->results->asso->freq[s]);
if(doMaf &32)
ksprintf(bufstr,"%f\t",pars->phat[s]);
if(doSNP){
if(doMaf &1)
ksprintf(bufstr,"%f\t",pars->results->freq->pmlSNP[s]);
if(doMaf &2)
ksprintf(bufstr,"%f\t",pars->results->freq->pEMSNP[s]);
if(doMaf &4)
ksprintf(bufstr,"%f\t",pars->results->freq->pmlunSNP[s]);
if(doMaf &8)
ksprintf(bufstr,"%f\t",pars->results->freq->pEMunSNP[s]);
}
kputw(pars->keepSites[s],bufstr);kputc('\n',bufstr);
}
pars->extras[index] = bufstr;
}
void abcFilterSNP::run(funkyPars *pars){
if(!doSnpStat)
return;
chunkyT *chk = pars->chk;
if(doSnpStat==1){
kstring_t *bufstr = new kstring_t;
bufstr->s=NULL;bufstr->l=bufstr->m=0;
//loop over sites;
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
//loop over samples
int cnts[4]={0,0,0,0};
for(int i=0;i<pars->nInd;i++){
tNode *nd = chk->nd[s][i];
if(nd==NULL)
continue;
for(int l=0;l<nd->l;l++){
int obB = refToInt[nd->seq[l]];
// fprintf(stderr,"%c ",nd.seq[l]);
int strand = (isupper(nd->seq[l])==0)<<1;
// fprintf(stderr,"strand:%d\n",strand);
if(obB==4)
continue;
if((obB!=pars->major[s] && obB!=pars->minor[s]) )
continue;
if(obB!=pars->major[s])
strand +=1;
//fprintf(stderr,"strand=%d\n",strand);
cnts[strand]++;
}
}
ksprintf(bufstr,"%s\t%d\t%d %d %d %d\t",header->target_name[pars->refId],pars->posi[s]+1, cnts[0],cnts[1],cnts[2],cnts[3]);
ksprintf(bufstr,"%f:%f:%f\t",sb1(cnts),sb2(cnts),sb3(cnts));
funkyHWE *hweStruct = (funkyHWE *) pars->extras[8];//THIS IS VERY NASTY! the ordering within general.cpp is now important
double lrt = 2*hweStruct->like0[s]-2*hweStruct->likeF[s];
double pval;
if(lrt<0)
pval =1;
else
pval =1- chi.cdf(lrt);
ksprintf(bufstr,"%f:%e\t",lrt,pval);
double Z = baseQbias(chk->nd[s],pars->nInd,refToInt[pars->major[s]],refToInt[pars->minor[s]]);
ksprintf(bufstr,"%f:%e\n",Z,2*phi(Z));
}
pars->extras[index] = bufstr;
}
}
static int stat_gettext(int tag, char *buf)
{
char *original_buf = buf;
/* TODO: Support more than one processors */
LARGE_INTEGER idle_time, kernel_time, user_time;
GetSystemTimes((FILETIME *)&idle_time, (FILETIME *)&kernel_time, (FILETIME *)&user_time);
uint64_t user = user_time.QuadPart / (TICKS_PER_SECOND / USER_HZ);
uint64_t nice = 0;
uint64_t system = kernel_time.QuadPart / (TICKS_PER_SECOND / USER_HZ);
uint64_t idle = idle_time.QuadPart / (TICKS_PER_SECOND / USER_HZ);
system -= idle; /* KernelTime includes IdleTime */
uint64_t iowait = 0;
uint64_t irq = 0;
uint64_t softirq = 0;
uint64_t steal = 0, guest = 0, guest_nice = 0;
buf += ksprintf(buf, "cpu %llu %llu %llu %llu %llu %llu %llu %llu %llu %llu\n",
user, nice, system, idle, iowait, irq, softirq, steal, guest, guest_nice);
buf += ksprintf(buf, "intr %llu\n", 0);
buf += ksprintf(buf, "swap %llu %llu\n", 0);
uint64_t ctxt = 0;
buf += ksprintf(buf, "ctxt %llu\n", ctxt);
/* Boot time */
SYSTEM_TIMEOFDAY_INFORMATION tod_info;
NtQuerySystemInformation(SystemTimeOfDayInformation, &tod_info, sizeof(tod_info), NULL);
uint64_t btime = filetime_to_unix_sec((FILETIME *)&tod_info.BootTime);
buf += ksprintf(buf, "btime %llu\n", btime);
uint64_t processes = 0;
buf += ksprintf(buf, "processes %llu\n", processes);
int procs_running = 1;
buf += ksprintf(buf, "procs_running %d\n", procs_running);
int procs_blocked = 0;
buf += ksprintf(buf, "procs_blocked %d\n", procs_blocked);
return buf - original_buf;
}
static void create_debug_thread(void)
{
static pthread_t test_tid;
char buf[80];
char * newstack;
errno = 0;
if ((newstack = sbrk(1024)) == (void *)-1) {
puts("Failed to create a stack\n");
return;
}
pthread_attr_t attr = {
.tpriority = 0,
.stackAddr = newstack,
.stackSize = 1024
};
errno = 0;
if (pthread_create(&test_tid, &attr, test_thread, 0)) {
puts("Thread creation failed\n");
return;
}
ksprintf(buf, sizeof(buf), "Thread created with id: %u\n", test_tid);
puts(buf);
}
static void * test_thread(void * arg)
{
while(1) {
sleep(1);
thread_stat();
}
}
static void thread_stat(void)
{
/* Print thread id & cpu mode */
char buf[80];
uint32_t mode, sp;
pthread_t id = pthread_self();
__asm__ volatile (
"mrs %0, cpsr\n\t"
"mov %1, sp"
: "=r" (mode), "=r" (sp));
ksprintf(buf, sizeof(buf), "My id: %u, sp: %u, my mode: %x\n", id, sp, mode);
puts(buf);
}
int main(int argc, char *argv[])
{
int i, ret;
double t_real;
kstring_t pg = {0,0,0};
t_real = realtime();
ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
bwa_pg = pg.s;
if (argc < 2) return usage();
if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
#ifdef USE_HTSLIB
if (strcmp(argv[1], "mem") != 0) {
err_fflush(stdout);
err_fclose(stdout);
}
#else
err_fflush(stdout);
err_fclose(stdout);
#endif
if (ret == 0) {
fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
fprintf(stderr, "[%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
}
free(bwa_pg);
return ret;
}
abcHaploCall::abcHaploCall(const char *outfiles,argStruct *arguments,int inputtype){
doHaploCall=0;
maxMis=-1;
minMinor=0;
doCount=0;
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doHaploCall")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
if(doHaploCall==0){
shouldRun[index] =0;
return;
}
//for kputs output
bufstr.s=NULL;bufstr.l=bufstr.m=0;
//make output files
const char* postfix;
postfix=".haplo.gz";
outfileZ = aio::openFileBG(outfiles,postfix);
//write header
bufstr.l=0;
ksprintf(&bufstr,"chr\tpos\tmajor");
for(int i=0;i<arguments->nInd;i++)
ksprintf(&bufstr,"\tind%d",i);
ksprintf(&bufstr,"\n");
aio::bgzf_write(outfileZ,bufstr.s,bufstr.l);
bufstr.l=0;
}
/**
* Get kmalloc'd array for full path name.
*/
static char * format_fpath(struct fatfs_inode * indir, const char * name)
{
char * fpath;
size_t fpath_size;
#ifdef configFATFS_DEBUG
KERROR(KERROR_DEBUG,
"format_fpath(indir \"%s\", name \"%s\")\n",
indir->in_fpath, name);
#endif
fpath_size = strlenn(name, NAME_MAX + 1) +
strlenn(indir->in_fpath, NAME_MAX + 1) + 6;
fpath = kmalloc(fpath_size);
if (!fpath)
return NULL;
ksprintf(fpath, fpath_size, "%s/%s", indir->in_fpath, name);
#ifdef configFATFS_DEBUG
KERROR(KERROR_DEBUG, "Formatted \"%s\" as \"%s\"\n",
name, fpath);
#endif
return fpath;
}
void call_stdout(marksplit_settings_t *settings, splitterhash_params_t *params, char *ffq_r1, char *ffq_r2)
{
kstring_t str1{0, 0, nullptr}, str2{0, 0, nullptr};
kstring_t final{0, 0, nullptr};
kputs((settings->gzip_output)? "zcat": "cat", &str1);
ks_resize(&str1, 1 << 10);
for(int i(0); i < settings->n_handles; ++i)
ksprintf(&str1, " %s", params->outfnames_r1[i]);
kputsnl(" | paste -d'~' - - - - ", &str1);
str2.s = dlib::kstrdup(&str1); // strdup the string.
for(uint32_t i(0); i < str2.l; ++i) {
LOG_DEBUG("Current str.s + i: %s.\n", str2.s + i);
if(memcmp(str2.s + i, "R1", 2) == 0)
str2.s[i + 1] = '2';
}
const char final_template[]{"pr -mts'~' <(%s) <(%s) | tr '~' '\\n'"};
ksprintf(&final, final_template, str1.s, str2.s);
dlib::bash_system(final.s);
free(str1.s), free(str2.s);
free(final.s);
}
void cat_fastqs(marksplit_settings_t *settings, splitterhash_params_t *params, char *ffq_r1, char *ffq_r2)
{
settings->is_se ? cat_fastqs_se(settings, params, ffq_r1)
: cat_fastqs_pe(settings, params, ffq_r1, ffq_r2);
}
/* Note the specific MTT version can also be used */
SkelUserReturn SkelUserGetModuleVersion(SkelDrvrModuleContext *mcon, char *mver)
{
if (mtt_ping(mcon))
return SkelUserReturnFAILED;
ksprintf(mver, "%d", mtt_readw(mcon, MTT_VHDL));
return SkelUserReturnOK;
}
void abcHWE::print(funkyPars *pars){
if(doHWE<=0)
return;
funkyHWE *hweStruct = (funkyHWE *) pars->extras[index];//new
bufstr.l=0;
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
float lrt= 2*hweStruct->like0[s]-2*hweStruct->likeF[s];
//DRAGON lrt is sometimes nan
float pval;
if(std::isnan(lrt))
pval=lrt;
else if(lrt<0)
pval=1;
else
pval=1-chisq->cdf(lrt);
// fprintf(stderr,"lrt:%f\n",lrt);
ksprintf(&bufstr,"%s\t%d\t%c\t%c\t%f\t%f\t%f\t%e\t%e\n",header->target_name[pars->refId],pars->posi[s]+1,intToRef[pars->major[s]],intToRef[pars->minor[s]],hweStruct->freqHWE[s],hweStruct->freq[s],hweStruct->F[s],lrt,pval);
}
aio::bgzf_write(outfileZ,bufstr.s,bufstr.l);bufstr.l=0;
}
// Added by JN
void abcSaf2::printSparse(funkyPars *p,int index,gzFile outfileSFS,gzFile outfileSFSPOS,char *chr){
realRes2 *r=(realRes2 *) p->extras[index];
int id=0;
// output site likelihoods in banded format
for(int i=0;i<p->numSites;i++){
if(r->oklist[i]==1){
gzwrite(outfileSFS,&r->offset[i],sizeof(int));
gzwrite(outfileSFS,&r->Kval[i],sizeof(int));
gzwrite(outfileSFS,r->pLikes[id++],sizeof(double)*r->Kval[i]);
}
}
kstring_t kbuf;kbuf.s=NULL;kbuf.l=kbuf.m=0;
for(int i=0;i<p->numSites;i++)
if(r->oklist[i]==1)
ksprintf(&kbuf,"%s\t%d\t%d\t%d\t%d\t%d\n",chr,p->posi[i]+1,r->offset[i],r->Kval[i],i,p->numSites);
else if (r->oklist[i]==2)
fprintf(stderr,"PROBS at: %s\t%d\n",chr,p->posi[i]+1);
gzwrite(outfileSFSPOS,kbuf.s,kbuf.l);
free(kbuf.s);
}
abcFilterSNP::abcFilterSNP(const char *outfiles,argStruct *arguments,int inputtype){
doSnpStat=0;
outfileZ = NULL;
if(arguments->argc==2){
if(!strcasecmp(arguments->argv[1],"-doSnpStat")||!strcasecmp(arguments->argv[1],"-doPost")){
printArg(stdout);
exit(0);
}else
return;
}
getOptions(arguments);
printArg(arguments->argumentFile);
if(doSnpStat==0){
shouldRun[index] =0;
return;
}
if(doSnpStat){
// fprintf(stderr,"running doSnpStat=%d\n",doSnpStat);
const char *postfix=".snpStat.gz";
outfileZ = aio::openFileBG(outfiles,postfix);
kstring_t bufstr;bufstr.s=NULL;bufstr.l=bufstr.m=0;
ksprintf(&bufstr,"Chromo\tPosition\t+Major +Minor -Major -Minor\tSB1:SB2:SB3\tHWE_LRT:HWE_pval\tbaseQ_Z:baseQ_pval\n");
aio::bgzf_write(outfileZ,bufstr.s,bufstr.l);bufstr.l=0;
free(bufstr.s);
}
}
int PLUGIN_GLOBAL(hfile_plugin_init,_libcurl)(struct hFILE_plugin *self)
{
static const struct hFILE_scheme_handler handler =
{ hopen_libcurl, hfile_always_remote, "libcurl", 50 };
const curl_version_info_data *info;
const char * const *protocol;
CURLcode err;
err = curl_global_init(CURL_GLOBAL_ALL);
if (err != CURLE_OK) { errno = easy_errno(NULL, err); return -1; }
curl.multi = curl_multi_init();
if (curl.multi == NULL) { curl_global_cleanup(); errno = EIO; return -1; }
info = curl_version_info(CURLVERSION_NOW);
ksprintf(&curl.useragent, "htslib/%s libcurl/%s",
hts_version(), info->version);
curl.nrunning = 0;
curl.perform_again = 0;
self->name = "libcurl";
self->destroy = libcurl_exit;
for (protocol = info->protocols; *protocol; protocol++)
hfile_add_scheme_handler(*protocol, &handler);
hfile_add_scheme_handler("s3", &handler);
hfile_add_scheme_handler("s3+http", &handler);
if (info->features & CURL_VERSION_SSL)
hfile_add_scheme_handler("s3+https", &handler);
return 0;
}
static int _log_exists(const char *dir, long long log_index, int *exists)
{
struct stat st;
char *path;
int ret = -1;
if ((path = ksprintf("%s/%lld", dir, log_index)) == NULL) {
perror("unco");
return -1;
}
if (lstat(path, &st) == 0) {
*exists = 1;
} else if (errno == ENOENT) {
*exists = 0;
} else {
kerr_printf("failed to stat file:%s", path);
goto Exit;
}
ret = 0;
Exit:
free(path);
return 0;
}
char *unco_get_default_dir(int (*default_mkdir)(const char *, mode_t))
{
char *home, *dir;
if ((dir = getenv("UNCO_HOME")) != NULL) {
// got it
if ((dir = strdup(dir)) == NULL) {
perror("unco");
return NULL;
}
} else {
// $HOME/.unco
if ((home = getenv("HOME")) == NULL) {
fprintf(stderr, "unco:$HOME is not set\n");
return NULL;
}
if ((dir = ksprintf("%s/.unco", home)) == NULL) {
perror("unco");
return NULL;
}
}
// mkdir
if (default_mkdir(dir, 0700) == 0 || errno == EEXIST) {
// ok
} else {
kerr_printf("failed to create dir:%s", dir);
free(dir);
return NULL;
}
return dir;
}
/**
* Copies contigs found in bcf header to another bcf header.
*/
void bcf_hdr_transfer_contigs(const bcf_hdr_t *hsrc, bcf_hdr_t *hdest)
{
vdict_t *d = (vdict_t*)hsrc->dict[BCF_DT_CTG];
int tid, m = kh_size(d);
const char **names = (const char**) calloc(m,sizeof(const char*));
int len[m];
khint_t k;
for (k=kh_begin(d); k<kh_end(d); k++)
{
if ( !kh_exist(d,k) ) continue;
tid = kh_val(d,k).id;
len[tid] = bcf_hrec_find_key(kh_val(d, k).hrec[0],"length");
int j;
if ( sscanf(kh_val(d, k).hrec[0]->vals[len[tid]],"%d",&j) )
len[tid] = j;
names[tid] = kh_key(d,k);
}
kstring_t s = {0,0,0};
for (tid=0; tid<m; tid++)
{
s.l = 0;
ksprintf(&s, "##contig=<ID=%s,length=%d>", names[tid], len[tid]);
bcf_hdr_append(hdest, s.s);
}
if (s.m) free(s.s);
}
static void ls(char ** args)
{
char * path = kstrtok(0, DELIMS, args);
int fildes, count;
struct dirent dbuf[10];
if (path == 0 || !strcmp(path, ""))
path = "./";
fildes = open(path, O_DIRECTORY | O_RDONLY | O_SEARCH);
if (fildes < 0) {
puts("Open failed\n");
return;
}
count = getdents(fildes, (char *)dbuf, sizeof(dbuf));
if (count < 0) {
puts("Reading directory entries failed\n");
}
for (int i = 0; i < count; i++) {
char buf[80];
struct stat stat;
fstatat(fildes, dbuf[i].d_name, &stat, 0);
ksprintf(buf, sizeof(buf), "%u %o %u:%u %s\n",
(uint32_t)dbuf[i].d_ino, (uint32_t)stat.st_mode,
(uint32_t)stat.st_uid, (uint32_t)stat.st_gid, dbuf[i].d_name);
puts(buf);
}
puts("\n");
close(fildes);
}
void KFMServer::slotExec( const char* _url, const char * _documents )
{
KURL u( _url );
if ( u.isMalformed() )
{
QString msg;
ksprintf(&msg, i18n( "The URL\n%s\nis malformed" ),
_url);
QMessageBox::warning( (QWidget*)0,
i18n( "KFM Error" ), msg );
return;
}
if ( _documents == 0L && _url != 0L )
{
KFMExec *e = new KFMExec;
e->openURL( _url );
return;
}
QString s( _documents );
QStrList urlList;
int i;
while ( ( i = s.find( "\n" ) ) != -1 )
{
QString t = s.left( i );
urlList.append( t.data() );
s = s.mid( i + 1, s.length() );
}
urlList.append( s.data() );
KMimeType *typ = KMimeType::getMagicMimeType( _url );
typ->runAsApplication( _url, &urlList );
}