/*
* Read a sequence from a FILE *fp of format "format". If "format" is 0
* (ANY_FORMAT), we automatically determine the correct format.
* We still pass a filename 'fn' although this isn't used other than for
* filling in the read->trace_name field.
*
* NB this function should NOT be used when Biolims support is required
* (as biolims readings are not stored in a file)
*
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *mfread_reading(mFILE *fp, char *fn, int format) {
Read *read;
mFILE *newfp;
if (!fn)
fn = "(unknown)";
newfp = freopen_compressed(fp, NULL);
if (newfp != fp) {
fp = newfp;
} else {
newfp = NULL;
}
#ifdef _WIN32
/*
* jkb 16/05/00 comment below
*
* On windows "prog < file.abi" will work wrongly (compared to
* "prog file.abi") because windows is rather stupid. It treats ascii
* and binary streams differently, it considers stdin to be ascii unless
* told otherwise, and it can only be told otherwise by using non-ansi
* windows-specific function calls.
*/
if (format != TT_EXP && format != TT_PLN && fp->fp)
_setmode(_fileno(fp->fp), _O_BINARY);
#endif
if (format == TT_ANY) {
format = fdetermine_trace_type(fp);
mrewind(fp);
}
switch (format) {
case TT_UNK:
case TT_ERR:
errout("File '%s' has unknown trace type\n", fn);
read = NULLRead;
break;
#ifdef IOLIB_SCF
case TT_SCF: {
Scf *scf;
scf = mfread_scf(fp);
if (scf) {
read = scf2read(scf);
scf_deallocate(scf);
} else
read = NULLRead;
break;
}
#endif
#ifdef IOLIB_CTF
case TT_CTF:
read = mfread_ctf(fp);
break;
#endif
#ifdef IOLIB_ZTR
case TT_ZTR:
case TT_ZTR1:
case TT_ZTR2:
case TT_ZTR3: {
ztr_t *ztr;
if ((ztr = mfread_ztr(fp))) {
uncompress_ztr(ztr);
read = ztr2read(ztr);
delete_ztr(ztr);
} else {
read = NULLRead;
}
break;
}
#endif
#ifdef IOLIB_ABI
case TT_ABI:
read = mfread_abi(fp);
break;
#endif
#ifdef IOLIB_ALF
case TT_ALF:
read = mfread_alf(fp);
break;
#endif
#ifdef IOLIB_EXP
case TT_EXP: {
/* FIXME: we shouldn't redirect like this */
Exp_info *e = exp_mfread_info(fp);
read = e ? exp2read(e,fn) : NULLRead;
break;
}
#endif
#ifdef IOLIB_PLN
case TT_PLN:
read = mfread_pln(fp);
break;
#endif
default:
errout("Unknown format %d specified to read_reading()\n", format);
read = NULLRead;
}
if (read != NULLRead && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
strcpy(read->trace_name, fn);
if (newfp) mfclose(newfp);
return read;
}
/*
* Ripped out of io_lib's trace_dump program.
* It reformats a trace to as printable ASCII.
*/
void dump_text(ztr_t *z, char *name, char mode, FILE **files) {
Read *read;
int i;
uncompress_ztr(z);
read = ztr2read(z); /* Inefficient; can do direct */
if (read == NULL) {
fprintf(stderr, "Tracedump was unable to open file %s\n", name );
return;
}
fprintf(files[0], "[Trace]\n");
fprintf(files[0], "%s\n", name);
fprintf(files[0], "\n[Header]\n");
fprintf(files[0], "%d\t\t# format\n", read->format);
fprintf(files[0], "%d\t\t# NPoints\n", read->NPoints);
fprintf(files[0], "%d\t\t# NBases\n", read->NBases);
fprintf(files[0], "%d\t\t# NFlows\n", read->nflows);
fprintf(files[0], "%d\t\t# maxTraceVal\n", (int)read->maxTraceVal-read->baseline);
fprintf(files[0], "%d\t\t# baseline\n", read->baseline);
fprintf(files[0], "%d\t\t# leftCutoff\n", read->leftCutoff);
fprintf(files[0], "%d\t\t# rightCutoff\n", read->rightCutoff);
fputs("\n[Bases]\n", files[0]);
for (i = 0; i < read->NBases; i++) {
fprintf(files[0], "%c %05d %+03d %+03d %+03d %+03d #%3d\n",
read->base[i],
read->basePos ? read->basePos[i] : 0,
(int)read->prob_A[i],
(int)read->prob_C[i],
(int)read->prob_G[i],
(int)read->prob_T[i],
i);
}
if (read->NPoints) {
fputs("\n[A_Trace]\n", files[0]);
for(i = 0; i < read->NPoints; i++)
fprintf(files[0], "%d\t#%5d\n", (int)read->traceA[i] - read->baseline, i);
fputs("\n[C_Trace]\n", files[0]);
for(i = 0; i < read->NPoints; i++)
fprintf(files[0], "%d\t#%5d\n", (int)read->traceC[i] - read->baseline, i);
fputs("\n[G_Trace]\n", files[0]);
for(i = 0; i < read->NPoints; i++)
fprintf(files[0], "%d\t#%5d\n", (int)read->traceG[i] - read->baseline, i);
fputs("\n[T_Trace]\n", files[0]);
for(i = 0; i < read->NPoints; i++)
fprintf(files[0], "%d\t#%5d\n", (int)read->traceT[i] - read->baseline, i);
}
if (read->flow_order) {
fputs("\n[Flows]\n", files[0]);
for (i = 0; i < read->nflows; i++) {
fprintf(files[0], "%c %5.2f %u\t#%5d\n",
read->flow_order[i],
read->flow ? read->flow[i] : 0,
read->flow_raw ? read->flow_raw[i] : 0,
i);
}
}
if (read->info) {
fputs("\n[Info]\n", files[0]);
fprintf(files[0], "%s\n", read->info);
}
read_deallocate(read);
}
/*
* As per partial_decode_ztr in srf.c, but without uncompress_ztr.
*/
ztr_t *partial_decode_ztr2(srf_t *srf, mFILE *mf, ztr_t *z) {
ztr_t *ztr;
ztr_chunk_t *chunk;
long pos = 0;
if (z) {
/* Use existing ZTR object => already loaded header */
ztr = z;
} else {
/* Allocate or use existing ztr */
if (NULL == (ztr = new_ztr()))
return NULL;
/* Read the header */
if (-1 == ztr_read_header(mf, &ztr->header)) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
/* Check magic number and version */
if (memcmp(ztr->header.magic, ZTR_MAGIC, 8) != 0) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
if (ztr->header.version_major != ZTR_VERSION_MAJOR) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
}
/* Load chunks */
pos = mftell(mf);
while ((chunk = ztr_read_chunk_hdr(mf))) {
chunk->data = (char *)xmalloc(chunk->dlength);
if (chunk->dlength != mfread(chunk->data, 1, chunk->dlength, mf))
break;
ztr->nchunks++;
ztr->chunk = (ztr_chunk_t *)xrealloc(ztr->chunk, ztr->nchunks *
sizeof(ztr_chunk_t));
memcpy(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
xfree(chunk);
pos = mftell(mf);
}
/*
* At this stage we're 'pos' into the mFILE mf with any remainder being
* a partial block.
*/
if (0 == ztr->nchunks) {
if (!z)
delete_ztr(ztr);
mrewind(mf);
return NULL;
}
/* Ensure we exit at the start of a ztr CHUNK */
mfseek(mf, pos, SEEK_SET);
/* If this is the header part, ensure we uncompress and init. data */
if (!z) {
/* Force caching of huffman code_sets */
ztr_find_hcode(ztr, CODE_USER);
/* And uncompress the rest */
uncompress_ztr(ztr);
}
return ztr;
}
/*
* Prints a read in solexa format. Depending on the given chunk type mode,
* only some of the chunks are printed out for every read. The files are
* given in the following order: seq, prb, sig2, int, nse. The files must
* already be open.
*/
void dump_solexa(ztr_t *z, char *name, char mode, FILE **files) {
int i, nc;
ztr_chunk_t **chunks;
char *seq;
int lane, tile, x, y;
parse_name(name, &lane, &tile, &x, &y);
uncompress_ztr(z);
chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
if (nc != 1) {
fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
return;
}
seq = chunks[0]->data+1;
/* Sequence */
if (mode & SEQ) {
fprintf(files[0], "%d\t%d\t%d\t%d\t%.*s\n",
lane, tile, x, y,
chunks[0]->dlength-1,
chunks[0]->data+1);
}
/* Confidence */
if (mode & PRB) {
chunks = ztr_find_chunks(z, ZTR_TYPE_CNF4, &nc);
if (nc != 1) {
fprintf(stderr, "Zero or greater than one CNF chunks found.\n");
return;
}
dump_conf4_solexa(files[1], seq, (sc *)chunks[0]->data+1,
chunks[0]->dlength-1);
}
/* Traces */
if (mode & SIG2) {
chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
for (i = 0; i < nc; i++) {
char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
if (!key || 0 == strcmp(key, "PROC")) {
key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
dump_samples4_solexa(files[2], lane, tile, x, y,
key ? atoi(key) : 0,
(uc *)chunks[i]->data+2,
chunks[i]->dlength-2);
break;
}
}
}
if (mode & INT) {
chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
for (i = 0; i < nc; i++) {
char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
if (key && 0 == strcmp(key, "SLXI")) {
key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
dump_samples4_solexa(files[3], lane, tile, x, y,
key ? atoi(key) : 0,
(uc *)chunks[i]->data+2,
chunks[i]->dlength-2);
break;
}
}
}
if (mode & NSE) {
chunks = ztr_find_chunks(z, ZTR_TYPE_SMP4, &nc);
for (i = 0; i < nc; i++) {
char *key = ztr_lookup_mdata_value(z, chunks[i], "TYPE");
if (key && 0 == strcmp(key, "SLXN")) {
key = ztr_lookup_mdata_value(z, chunks[i], "OFFS");
dump_samples4_solexa(files[4], lane, tile, x, y,
key ? atoi(key) : 0,
(uc *)chunks[i]->data+2,
chunks[i]->dlength-2);
break;
}
}
}
}
