static __host__ __device__ Tout _pixDist_CN(Tin &pix1, Tin &pix2)
{
return Tout(SQR(pix1.x - pix2.x) + SQR(pix1.y - pix2.y) + SQR(pix1.z - pix2.z) + SQR(pix1.w - pix2.w));
}};
int bamvalidateTemplate(::libmaus2::util::ArgInfo const & arginfo)
{
libmaus2::timing::RealTimeClock rtc; rtc.start();
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
bool const basequalhist = arginfo.getValue("basequalhist",getDefaultBaseQualHist());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
arginfo,false // put rank
)
);
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();
// add PG line to header
std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
header.text,
"bamvalidate", // ID
"bamvalidate", // PN
arginfo.commandline, // CL
::libmaus2::bambam::ProgramHeaderLineSet(header.text).getLastIdInChain(), // PP
std::string(PACKAGE_VERSION) // VN
);
// construct new header
::libmaus2::bambam::BamHeader uphead(upheadtext);
/*
* start index/md5 callbacks and alignment writer
*/
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pout;
if ( passthrough )
{
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Tout (
libmaus2::bambam::BamBlockWriterBaseFactory::construct(uphead, arginfo, Pcbs)
);
Pout = UNIQUE_PTR_MOVE(Tout);
}
libmaus2::autoarray::AutoArray<char> lastvalidname(256); // max valid read name is 255 bytes
uint64_t alsok = 0;
::libmaus2::autoarray::AutoArray<char> qual;
libmaus2::autoarray::AutoArray<uint64_t> H(static_cast<uint64_t>(std::numeric_limits<uint8_t>::max())+1);
std::fill(H.begin(),H.end(),0ull);
try
{
while ( dec.readAlignment() )
{
if ( passthrough )
Pout->writeAlignment(algn);
if ( basequalhist )
{
uint64_t const l = algn.getLseq();
uint8_t const * Qc = libmaus2::bambam::BamAlignmentDecoderBase::getQual(algn.D.begin());
uint8_t const * const Qe = Qc + l;
while ( Qc != Qe )
H[*(Qc++)]++;
}
uint64_t const lname = algn.getLReadName();
char const * name = algn.getName();
std::copy(name,name+lname+1,lastvalidname.begin());
alsok += 1;
}
}
catch(std::exception const & ex)
{
std::cerr << "[E] name of last valid alignment was " << lastvalidname.begin() << std::endl;
std::cerr << "[E] read " << alsok << " valid alignments" << std::endl;
throw;
}
Pout.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
if ( verbose )
std::cerr << "[V] checked " << alsok << " alignments in " << rtc.formatTime(rtc.getElapsedSeconds())
<< " (" << alsok / rtc.getElapsedSeconds() << " al/s)" << std::endl;
if ( basequalhist )
{
uint64_t const s = std::accumulate(H.begin(),H.end(),0ull);
uint64_t a = 0;
uint64_t minq = std::numeric_limits<uint64_t>::max();
uint64_t maxq = 0;
for ( uint64_t i = 0; i < H.size(); ++i )
if ( H[i] )
{
minq = std::min(minq,i);
maxq = std::max(maxq,i);
a += H[i];
std::cerr
<< "[H]\t" << i << "\t";
if ( ( static_cast<uint64_t>(i+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(i+33)) )
std::cerr << static_cast<char>(i+33);
std::cerr << "\t"
<< H[i] << "\t"
<< (H[i] / static_cast<double>(s)) << "\t"
<< (a / static_cast<double>(s))
<< std::endl;
}
if ( s )
{
std::cerr << "[H]\tmin\t" << minq << "\t";
if ( ( static_cast<uint64_t>(minq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(minq+33)) )
std::cerr << static_cast<char>(minq+33);
std::cerr << std::endl;
std::cerr << "[H]\tmax\t" << maxq << "\t";
if ( ( static_cast<uint64_t>(maxq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(maxq+33)) )
std::cerr << static_cast<char>(maxq+33);
std::cerr << std::endl;
}
}
return EXIT_SUCCESS;
}
static __host__ __device__ Tout _pixDist_CN(Tin &pix1, Tin &pix2)
{
return Tout(SQR(pix1.x - pix2.x));
}};
/*
* mail [ -ehpPqrtw ] [-x debuglevel] [ -f file ] [ -F user(s) ]
* mail -T file persons
* mail [ -tw ] [ -m messagetype ] persons
* rmail [ -tw ] persons
*/
int
main(int argc, char **argv)
{
register int i;
char *cptr, *p;
static char pn[] = "main";
extern char **environ;
int env_var_idx, next_slot_idx;
int tmpfd = -1;
(void)&argc;
(void)&argv;
setlocale(LC_CTYPE, "");
mb_cur_max = MB_CUR_MAX;
/* fix here for bug #1086130 - security hole */
/* skip over the LD_* env variable */
env_var_idx = 0;
next_slot_idx = 0;
while (environ[env_var_idx] != NULL) {
environ[next_slot_idx] = environ[env_var_idx];
if (strncmp(environ[env_var_idx], "LD_", 3)) {
next_slot_idx++;
}
env_var_idx++;
}
environ[next_slot_idx] = NULL;
line = smalloc(linesize = LSIZE);
*line = '\0';
#ifdef SIGCONT
{
struct sigaction nsig;
nsig.sa_handler = SIG_DFL;
sigemptyset(&nsig.sa_mask);
nsig.sa_flags = SA_RESTART;
sigaction(SIGCONT, &nsig, (struct sigaction *)0);
}
#endif
/*
* Strip off path name of this command for use in messages
*/
if ((program = strrchr(argv[0], '/')) != NULL) {
program++;
} else {
program = argv[0];
}
/* Close all file descriptors except stdin, stdout & stderr */
for (i = 3; close(i) == 0; i++);
/*
* Get group id for mail, exit if none exists
*/
if ((grpptr = getgrnam("mail")) == NULL) {
errmsg(E_GROUP, "");
exit(1);
} else {
mailgrp = grpptr->gr_gid;
}
/*
* Save the *id for later use.
*/
my_uid = getuid();
my_gid = getgid();
my_euid = geteuid();
my_egid = getegid();
/*
* What command (rmail or mail)?
*/
if (strcmp(program, "rmail") == SAME) {
ismail = FALSE;
}
/*
* Parse the command line and adjust argc and argv
* to compensate for any options
*/
i = parse(argc, argv);
argv += (i - 1);
argc -= (i - 1);
/* block a potential security hole */
if (flgT && (my_euid != 0)) {
setgid(my_gid);
Tout(pn, "Setgid unset\n");
}
if (debug == 0) {
/* If not set as an invocation option, check for system-wide */
/* global flag */
char *xp = xgetenv("DEBUG");
if (xp != (char *)NULL) {
debug = atoi(xp);
if (debug < 0) {
/* Keep trace file even if successful */
keepdbgfile = -1;
debug = -debug;
}
}
}
if (debug > 0) {
strcpy(dbgfname, "/tmp/MLDBGXXXXXX");
if ((tmpfd = mkstemp(dbgfname)) == -1) {
fprintf(stderr, "%s: can't open debugging file '%s'\n",
program, dbgfname);
exit(13);
}
if ((dbgfp = fdopen(tmpfd, "w")) == (FILE *)NULL) {
fprintf(stderr, "%s: can't open debugging file '%s'\n",
program, dbgfname);
close(tmpfd);
exit(13);
}
setbuf(dbgfp, NULL);
fprintf(dbgfp, "main(): debugging level == %d\n", debug);
fprintf(dbgfp, "main(): trace file ='%s': kept %s\n", dbgfname,
((keepdbgfile < 0) ?
"on success or failure." : "only on failure."));
}
if (!ismail && (goerr > 0 || !i)) {
Dout(pn, 11, "!ismail, goerr=%d, i=%d\n", goerr, i);
if (goerr > 0) {
errmsg(E_SYNTAX, "Usage: rmail [-wt] person(s)");
}
if (!i) {
errmsg(E_SYNTAX, "At least one user must be specified");
}
Dout(pn, 11, "exiting!\n");
done(0);
}
umsave = umask(7);
uname(&utsn);
if ((p = xgetenv("CLUSTER")) != (char *)NULL) {
/*
* We are not who we appear...
*/
thissys = p;
} else {
thissys = utsn.nodename;
}
Dout(pn, 11, "thissys = '%s', uname = '%s'\n", thissys, utsn.nodename);
failsafe = xgetenv("FAILSAFE");
if (failsafe)
Dout(pn, 11, "failsafe processing enabled to %s\n", failsafe);
/*
* Use environment variables
*/
home = getenv("HOME");
if (!home || !*home) {
home = ".";
}
pwd = getpwuid(my_uid);
if (pwd)
cpy(&my_name, &my_namesize, pwd->pw_name);
else
cpy(&my_name, &my_namesize, "");
/* If root, use LOGNAME if set */
if (my_uid == 0) {
/* If root, use LOGNAME if set */
if (((cptr = getenv("LOGNAME")) != NULL) &&
(strlen(cptr) != 0)) {
cpy(&my_name, &my_namesize, cptr);
}
}
Dout(pn, 11, "my_name = '%s'\n", my_name);
/*
* Catch signals for cleanup
*/
if (setjmp(sjbuf)) {
done(0);
}
setsig(SIGINT, delete);
setsig(SIGQUIT, delete);
setsig(SIGTRAP, delete);
#ifdef SIGIOT
setsig(SIGIOT, delete);
#endif
#ifdef SIGEMT
setsig(SIGEMT, delete);
#endif
setsig(SIGBUS, delete);
setsig(SIGSEGV, delete);
setsig(SIGPIPE, delete);
setsig(SIGALRM, delete);
setsig(SIGHUP, sig_done);
setsig(SIGTERM, sig_done);
cksaved(my_name);
/*
* Rmail is always invoked to send mail
*/
Dout(pn, 11, "ismail=%d, argc=%d\n", ismail, argc);
if (ismail && (argc == 1)) {
sending = FALSE;
printmail();
} else {
sending = TRUE;
sendmail(argc, argv);
}
done(0);
/*NOTREACHED*/
return 0;
}
