int list_contents(CIFBLK *cif, char *volser, DSXTENT *extent)
{
u_int cext = 0;
u_int ccyl = (extent[cext].xtbcyl[0] << 8) | extent[cext].xtbcyl[1];
u_int chead = (extent[cext].xtbtrk[0] << 8) | extent[cext].xtbtrk[1];
u_int ecyl = (extent[cext].xtecyl[0] << 8) | extent[cext].xtecyl[1];
u_int ehead = (extent[cext].xtetrk[0] << 8) | extent[cext].xtetrk[1];
#ifdef EXTERNALGUI
if (extgui) fprintf(stderr,"ETRK=%d\n",((ecyl*(cif->heads))+ehead));
#endif /*EXTERNALGUI*/
printf("%s%s: VOLSER=%s\n", needsep ? "\n" : "", cif->fname, volser);
needsep = 1;
do {
BYTE *ptr;
int rc = read_track(cif, ccyl, chead);
#ifdef EXTERNALGUI
if (extgui) fprintf(stderr,"CTRK=%d\n",((ccyl*(cif->heads))+chead));
#endif /*EXTERNALGUI*/
if (rc < 0)
return -1;
ptr = cif->trkbuf + CKDDASD_TRKHDR_SIZE;
while (!end_of_track(ptr))
{
char dsname[45];
CKDDASD_RECHDR *rechdr = (CKDDASD_RECHDR*)ptr;
int kl = rechdr->klen;
int dl = (rechdr->dlen[0] << 8) | rechdr->dlen[1];
make_asciiz(dsname, sizeof(dsname), ptr + CKDDASD_RECHDR_SIZE, kl);
dsname[44] = '\0';
if ( valid_dsname( dsname ) )
printf("%s\n", dsname);
ptr += CKDDASD_RECHDR_SIZE + kl + dl;
}
chead++;
if (chead >= cif->heads) {
ccyl++;
chead = 0;
}
} while (ccyl < ecyl || (ccyl == ecyl && chead <= ehead));
return 0;
}
static int track_action(expression_t *arg, sgen_ctx_t *c) {
if (c->num_tracks == 0) { c->tracks = malloc(sizeof(track_t)); }
++c->num_tracks;
c->tracks = realloc(c->tracks, c->num_tracks*sizeof(track_t));
track_t t;
if (!read_track(arg, &t, c)) return 0;
c->tracks[c->num_tracks-1] = t;
return 1;
}
/*
* Read in a midi file from the specified open file pointer, fp
* and return an mtree structure tree representing the file.
*
* Arguments:
* fp - Input file pointer
*/
struct rootElement *
midi_read(FILE *fp)
{
struct midistate mState;
struct midistate *msp;
struct rootElement *root;
struct element *el;
int i;
msp = &mState;
msp->fp = fp;
msp->tempo_map = md_tempomap_new();
msp->notes = g_ptr_array_new();
msp->port = 0;
root = read_head(msp);
md_add(MD_CONTAINER(root), NULL); /* Leave room for the tempo map */
for (i = 0; i < root->tracks; i++) {
el = MD_ELEMENT(read_track(msp));
/* If format 1 then the first track is really the tempo map */
if (root->format == 1
&& i == 0
&& MD_CONTAINER(el)->elements->len == 0) {
/* It will be added after the loop */
md_free(el);
continue;
}
md_add(MD_CONTAINER(root), el);
}
g_ptr_array_index(MD_CONTAINER(root)->elements, 0) = msp->tempo_map;
msp->tempo_map = NULL;
g_ptr_array_free(msp->notes, 1);
return root;
}
int runFishhook(int argc, char** argv) {
parseFishOptions(argc, argv);
if (opt::verbose) {
std::cerr << "FishHook Params: " << std::endl
<< "\tWidth: " << SeqLib::AddCommas(opt::width) << std::endl
<< "\tEvents: " << opt::events << std::endl
<< "\tCoverage Mask: " << opt::coverage << std::endl
<< "\tSlop: " << SeqLib::AddCommas(opt::slop) << std::endl
<< "\tInterval Tracks: " << std::endl;
for (auto& i : opt::interval_files)
std::cerr << "\t-- " << i << std::endl;
std::cerr << "\tScored Tracks: " << std::endl;
for (auto& i : opt::scored_files)
std::cerr << "\t-- " << i << std::endl;
std::cerr << "\tSequence Features: " << std::endl;
for (auto& i : opt::seq_features)
std::cerr << "\t-- " << i << std::endl;
}
// read in the covariate tracks
SeqHashMap<std::string, Fractions> intervals;
// read a header for info
SeqLib::BamReader rdr;
if (!rdr.Open(opt::bam)) {
std::cerr << "Error: Could not read BAM supplied by -b: " << opt::bam << std::endl;
exit(EXIT_FAILURE);
}
hdr = rdr.Header();
// read in the reference genome
SeqLib::RefGenome ref;
if (!ref.LoadIndex(opt::refgenome)) {
if (opt::seq_features.size()) {
std::cerr << "Error: Could not read referene genome supplied by -G: " << opt::refgenome << std::endl;
exit(EXIT_FAILURE);
}
}
// read in the events
if (opt::verbose) std::cerr << "...reading events " << opt::events << std::endl;
EventList events;
if (!events.readFromBed(opt::events, hdr)) {
std::cerr << "Error: Could not read events BED: " << opt::events << std::endl;
exit(EXIT_FAILURE);
}
if (opt::verbose) std::cerr << "...read in " << SeqLib::AddCommas(events.size()) << " events" << std::endl;
events.CreateTreeMap();
// create the tiled regions
FishHookTiles fish(opt::width, opt::slop, hdr.GetHeaderSequenceVector());
if (opt::verbose)
std::cerr << "...constructed " << SeqLib::AddCommas(fish.size()) << " fishhook intervals" << std::endl;
fish.CreateTreeMap();
// read the coverage mask
SeqLib::GRC cov;
if (!opt::coverage.empty()) {
if (opt::verbose) std::cerr << "...reading coverage mask " << opt::coverage << std::endl;
cov.ReadBED(opt::coverage, hdr);
if (opt::verbose) std::cerr << "...read in " << SeqLib::AddCommas(cov.size()) << " covered regions " << std::endl;
if (!cov.size()) {
std::cerr << "Non-empty coverage track read with 0 regions. Check that is non-empty BED" << std::endl;
exit(EXIT_FAILURE);
}
if (opt::verbose) std::cerr << "...creating interval tree map on covered regions and overlapping with tiles" << std::endl;
cov.CreateTreeMap();
// find covered amount per tile
std::vector<int32_t> q, s;
SeqLib::GRC ovlp;
// fish is subject
if (fish.size() > cov.size()) // do in most efficient order
ovlp = cov.FindOverlaps(fish, q, s, false);
else
ovlp = fish.FindOverlaps(cov, s, q, false);
if (opt::verbose) std::cerr << "..." << SeqLib::AddCommas(ovlp.size()) << " regions are covered" << std::endl;
// set the amount covered by each
for (size_t i = 0; i < ovlp.size(); ++i) {
fish[s[i]].covered += (double)ovlp[i].Width() / fish[s[i]].Width();
}
// mask the events
q.clear(); s.clear(); ovlp.clear();
// events is subject
if (events.size() > cov.size()) // do in most efficient order
ovlp = cov.FindOverlaps(events, q, s, false);
else
ovlp = events.FindOverlaps(cov, s, q, false);
EventList newe;
// set the amount covered by each
for (size_t i = 0; i < ovlp.size(); ++i) {
newe.add(Event(ovlp[i], events.at(s[i]).id));
}
events = newe;
events.CreateTreeMap();
if (opt::verbose) std::cerr << "...kept " << SeqLib::AddCommas(events.size()) << " events after mask" << std::endl;
} else {
for (auto& i : fish)
i.covered = 1; // the entire thing is covered if no mask provided
}
// read in the interval tracks
for (auto& i : opt::interval_files)
read_track(i, intervals, cov, false);
for (auto& i : opt::scored_files)
read_track(i, intervals, cov, true);
// count events per tile (also de-dupes on patient per bin)
fish.CountEvents(events);
// overlap the covariates with the tiles
for (auto& i : intervals) {
fish.AddIntervalCovariate(i.first, i.second);
}
// make the matrix
FishModel fm;
fm.AddTiles(fish);
fm.SetNumThreads(opt::num_threads);
fm.EstimateOLS();
fm.CooksDistance(fm.GetOLS());
// write the covariates
fish.PrintBEDHeader(std::cout);
fish.PrintBED(std::cout, hdr);
return 0;
}
