int
main(int argc, char **argv) {
char *gkpStoreName = NULL;
char *outPrefix = NULL;
char *clrName = NULL;
uint32 libToDump = 0;
uint32 bgnID = 1;
uint32 endID = UINT32_MAX;
bool dumpAllReads = false;
bool dumpAllBases = false;
bool dumpOnlyDeleted = false;
bool dumpFASTQ = true;
bool dumpFASTA = false;
bool withLibName = true;
argc = AS_configure(argc, argv);
int arg = 1;
int err = 0;
while (arg < argc) {
if (strcmp(argv[arg], "-G") == 0) {
gkpStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-o") == 0) {
outPrefix = argv[++arg];
} else if (strcmp(argv[arg], "-c") == 0) {
clrName = argv[++arg];
} else if (strcmp(argv[arg], "-l") == 0) {
libToDump = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-b") == 0) {
bgnID = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-e") == 0) {
endID = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-r") == 0) {
bgnID = atoi(argv[++arg]);
endID = bgnID;
} else if (strcmp(argv[arg], "-allreads") == 0) {
dumpAllReads = true;
} else if (strcmp(argv[arg], "-allbases") == 0) {
dumpAllBases = true;
} else if (strcmp(argv[arg], "-onlydeleted") == 0) {
dumpOnlyDeleted = true;
dumpAllReads = true; // Otherwise we won't report the deleted reads!
} else if (strcmp(argv[arg], "-fastq") == 0) {
dumpFASTQ = true;
dumpFASTA = false;
} else if (strcmp(argv[arg], "-fasta") == 0) {
dumpFASTQ = false;
dumpFASTA = true;
} else if (strcmp(argv[arg], "-nolibname") == 0) {
withLibName = false;
} else {
err++;
fprintf(stderr, "ERROR: unknown option '%s'\n", argv[arg]);
}
arg++;
}
if (gkpStoreName == NULL)
err++;
if (outPrefix == NULL)
err++;
if (err) {
fprintf(stderr, "usage: %s [...] -o fastq-prefix -g gkpStore\n", argv[0]);
fprintf(stderr, " -G gkpStore\n");
fprintf(stderr, " -o fastq-prefix write files fastq-prefix.(libname).fastq, ...\n");
fprintf(stderr, "\n");
fprintf(stderr, " -l libToDump output only read in library number libToDump (NOT IMPLEMENTED)\n");
fprintf(stderr, " -b id output starting at read 'id'\n");
fprintf(stderr, " -e id output stopping after read 'id'\n");
fprintf(stderr, "\n");
fprintf(stderr, " -c clearFile clear range file from OBT modules\n");
fprintf(stderr, " -allreads if a clear range file, lower case mask the deleted reads\n");
fprintf(stderr, " -allbases if a clear range file, lower case mask the non-clear bases\n");
fprintf(stderr, " -onlydeleted if a clear range file, only output deleted reads (the entire read)\n");
fprintf(stderr, "\n");
fprintf(stderr, " -r id output only the single read 'id'\n");
fprintf(stderr, "\n");
fprintf(stderr, " -fastq output is FASTQ format (with extension .fastq, default)\n");
fprintf(stderr, " -fasta output is FASTA format (with extension .fasta)\n");
fprintf(stderr, "\n");
fprintf(stderr, " -nolibname don't include the library name in the output file name\n");
fprintf(stderr, "\n");
if (gkpStoreName == NULL)
fprintf(stderr, "ERROR: no gkpStore (-G) supplied.\n");
if (outPrefix == NULL)
fprintf(stderr, "ERROR: no output prefix (-o) supplied.\n");
exit(1);
}
gkStore *gkpStore = new gkStore(gkpStoreName);
uint32 numReads = gkpStore->gkStore_getNumReads();
uint32 numLibs = gkpStore->gkStore_getNumLibraries();
clearRangeFile *clrRange = (clrName == NULL) ? NULL : new clearRangeFile(clrName, gkpStore);
if (bgnID < 1)
bgnID = 1;
if (numReads < endID)
endID = numReads;
if (endID < bgnID)
fprintf(stderr, "No reads to dump; reversed ranges make no sense: bgn="F_U32" end="F_U32"??\n", bgnID, endID);
fprintf(stderr, "Dumping reads from %u to %u (inclusive).\n", bgnID, endID);
libOutput **out = new libOutput * [numLibs + 1];
// Allocate outputs. If withLibName == false, all reads will artificially be in lib zero, the
// other files won't ever be created. Otherwise, the zeroth file won't ever be created.
out[0] = new libOutput(outPrefix, NULL);
for (uint32 i=1; i<=numLibs; i++)
out[i] = new libOutput(outPrefix, gkpStore->gkStore_getLibrary(i)->gkLibrary_libraryName());
// Grab a new readData, and iterate through reads to dump.
gkReadData *readData = new gkReadData;
for (uint32 rid=bgnID; rid<=endID; rid++) {
gkRead *read = gkpStore->gkStore_getRead(rid);
uint32 libID = (withLibName == false) ? 0 : read->gkRead_libraryID();
uint32 lclr = 0;
uint32 rclr = read->gkRead_sequenceLength();
bool ignore = false;
//fprintf(stderr, "READ %u claims id %u length %u in lib %u\n", rid, read->gkRead_readID(), read->gkRead_sequenceLength(), libID);
// If a clear range file is supplied, grab the clear range. If it hasn't been set, the default
// is the entire read.
if (clrRange) {
lclr = clrRange->bgn(rid);
rclr = clrRange->end(rid);
ignore = clrRange->isDeleted(rid);
}
// Abort if we're not dumping anything from this read
// - not in a library we care about
// - deleted, and not dumping all reads
// - not deleted, but only reporting deleted reads
if (((libToDump != 0) && (libID == libToDump)) ||
((dumpAllReads == false) && (ignore == true)) ||
((dumpOnlyDeleted == true) && (ignore == false)))
continue;
// And if we're told to ignore the read, and here, then the read was deleted and we're printing
// all reads. Reset the clear range to the whole read, the clear range is invalid.
if (ignore) {
rclr = read->gkRead_sequenceLength();
lclr = 0;
}
// Grab the sequence and quality.
gkpStore->gkStore_loadReadData(read, readData);
char *seq = readData->gkReadData_getSequence();
char *qlt = readData->gkReadData_getQualities();
uint32 len = rclr - lclr;
// Soft mask not-clear bases
if (dumpAllBases == true) {
for (uint32 i=0; i<lclr; i++)
seq[i] += (seq[i] >= 'A') ? 'a' - 'A' : 0;
for (uint32 i=lclr; i<rclr; i++)
seq[i] += (seq[i] >= 'A') ? 0 : 'A' - 'a';
for (uint32 i=rclr; seq[i]; i++)
seq[i] += (seq[i] >= 'A') ? 'a' - 'A' : 0;
rclr = read->gkRead_sequenceLength();
lclr = 0;
}
// Chop off the ends we're not printing.
seq += lclr;
seq[len] = 0;
qlt[len] = 0;
// And print the read.
if (dumpFASTQ)
AS_UTL_writeFastQ(out[libID]->getFASTQ(), seq, len, qlt, len,
"@"F_U32" clr="F_U32","F_U32"\n",
rid, lclr, rclr);
if (dumpFASTA)
AS_UTL_writeFastA(out[libID]->getFASTA(), seq, len, 0,
">"F_U32" clr="F_U32","F_U32"\n",
rid, lclr, rclr);
}
delete readData;
for (uint32 i=1; i<=numLibs; i++)
delete out[i];
delete [] out;
delete gkpStore;
exit(0);
}
int
main(int argc, char **argv) {
char *gkpStoreName = NULL;
char *outPrefix = NULL;
AS_IID libToDump = 0;
uint32 clrToDump = AS_READ_CLEAR_LATEST;
AS_IID bgnIID = 1;
AS_IID endIID = AS_IID_MAX;
bool dumpAllBases = true;
bool dumpAllReads = false;
argc = AS_configure(argc, argv);
int arg = 1;
int err = 0;
while (arg < argc) {
if (strcmp(argv[arg], "-l") == 0) {
libToDump = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-b") == 0) {
bgnIID = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-e") == 0) {
endIID = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-c") == 0) {
clrToDump = gkStore_decodeClearRegionLabel(argv[++arg]);
} else if (strcmp(argv[arg], "-g") == 0) {
gkpStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-o") == 0) {
outPrefix = argv[++arg];
} else {
err++;
fprintf(stderr, "ERROR: unknown option '%s'\n", argv[arg]);
}
arg++;
}
if (gkpStoreName == NULL)
err++;
if (outPrefix == NULL)
err++;
if (clrToDump == AS_READ_CLEAR_ERROR)
err++;
if (err) {
fprintf(stderr, "usage: %s [...] -o fastq-prefix -g gkpStore\n", argv[0]);
fprintf(stderr, " -g gkpStore\n");
fprintf(stderr, " -o fastq-prefix write files fastq-prefix.1.fastq, fastq-prefix.2.fastq, fastq-prefix.paired.fastq, fastq-prefix.unmated.fastq\n");
fprintf(stderr, " \n");
fprintf(stderr, " -l libToDump output only fragments in library number libToDump (NOT IMPLEMENTED)\n");
fprintf(stderr, " -b iid output starting at fragment iid\n");
fprintf(stderr, " -e iid output stopping after fragment iid\n");
fprintf(stderr, " -c clrName output clear range 'clrName'\n");
fprintf(stderr, " \n");
if (gkpStoreName == NULL)
fprintf(stderr, "ERROR: no gkpStore (-g) supplied.\n");
if (outPrefix == NULL)
fprintf(stderr, "ERROR: no output prefix (-o) supplied.\n");
if (clrToDump == AS_READ_CLEAR_ERROR)
fprintf(stderr, "ERROR: clear range (-c) is not a valid clear range.\n");
exit(1);
}
gkStore *gkp = new gkStore(gkpStoreName, FALSE, FALSE);
AS_IID numFrags = gkp->gkStore_getNumFragments();
AS_IID numLibs = gkp->gkStore_getNumLibraries();
libInfo **lib = new libInfo * [numLibs];
lib[0] = new libInfo(outPrefix, "legacy");
for (uint32 i=1; i<numLibs; i++)
lib[i] = new libInfo(outPrefix, gkp->gkStore_getLibrary(i)->libraryName);
if (bgnIID < 1)
bgnIID = 1;
if (numFrags < endIID)
endIID = numFrags;
//AS_IID streamBgn = AS_IID_MIN;
//AS_IID streamEnd = AS_IID_MAX;
gkStream *fs = new gkStream(gkp, bgnIID, endIID, GKFRAGMENT_QLT);
gkFragment fr;
while (fs->next(&fr)) {
int32 lclr = fr.gkFragment_getClearRegionBegin(clrToDump);
int32 rclr = fr.gkFragment_getClearRegionEnd (clrToDump);
AS_IID id1 = fr.gkFragment_getReadIID();
AS_IID id2 = fr.gkFragment_getMateIID();
AS_IID libIID = fr.gkFragment_getLibraryIID();
if ((dumpAllReads == false) && (fr.gkFragment_getIsDeleted() == true))
// Fragment is deleted, don't dump.
continue;
if ((libToDump != 0) && (fr.gkFragment_getLibraryIID() == libToDump))
// Fragment isn't marked for dumping, don't dump.
continue;
if ((dumpAllBases == false) && (lclr >= rclr))
// Fragment has null or invalid clear range, don't dump.
continue;
if ((id2 != 0) && (id2 < id1))
// Mated, and the mate is the first frag. We've already reported this one.
continue;
char *seq = fr.gkFragment_getSequence() + ((dumpAllBases == false) ? fr.gkFragment_getClearRegionBegin(clrToDump) : 0);
char *qlt = fr.gkFragment_getQuality() + ((dumpAllBases == false) ? fr.gkFragment_getClearRegionBegin(clrToDump) : 0);
int32 len = (dumpAllBases == false) ? fr.gkFragment_getClearRegionLength(clrToDump) : fr.gkFragment_getSequenceLength();
seq[len] = 0;
qlt[len] = 0;
if (dumpAllBases == true) {
for (uint32 i=0; i<lclr; i++)
seq[i] += (seq[i] >= 'A') ? 'a' - 'A' : 0;
for (uint32 i=lclr; i<rclr; i++)
seq[i] += (seq[i] >= 'A') ? 0 : 'A' - 'a';
for (uint32 i=rclr; seq[i]; i++)
seq[i] += (seq[i] >= 'A') ? 'a' - 'A' : 0;
}
if (id2 == 0) {
// Unmated read, dump to the unmated reads file.
AS_UTL_writeFastQ(lib[libIID]->u, seq, len, qlt, len,
"@%s clr="F_U32","F_U32" clv="F_U32","F_U32" max="F_U32","F_U32" tnt="F_U32","F_U32" rnd=%c\n",
AS_UID_toString(fr.gkFragment_getReadUID()),
fr.gkFragment_getClearRegionBegin(clrToDump),
fr.gkFragment_getClearRegionEnd (clrToDump),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_TNT),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_TNT),
fr.gkFragment_getIsNonRandom() ? 'f' : 't');
continue;
}
// Write the first fragment (twice).
AS_UTL_writeFastQ(lib[libIID]->a, seq, len, qlt, len,
"@%s clr="F_U32","F_U32" clv="F_U32","F_U32" max="F_U32","F_U32" tnt="F_U32","F_U32" rnd=%c\n",
AS_UID_toString(fr.gkFragment_getReadUID()),
fr.gkFragment_getClearRegionBegin(clrToDump),
fr.gkFragment_getClearRegionEnd (clrToDump),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_TNT),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_TNT),
fr.gkFragment_getIsNonRandom() ? 'f' : 't');
AS_UTL_writeFastQ(lib[libIID]->p, seq, len, qlt, len,
"@%s clr="F_U32","F_U32" clv="F_U32","F_U32" max="F_U32","F_U32" tnt="F_U32","F_U32" rnd=%c\n",
AS_UID_toString(fr.gkFragment_getReadUID()),
fr.gkFragment_getClearRegionBegin(clrToDump),
fr.gkFragment_getClearRegionEnd (clrToDump),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_TNT),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_TNT),
fr.gkFragment_getIsNonRandom() ? 'f' : 't');
// Grab the second fragment.
gkp->gkStore_getFragment(id2, &fr, GKFRAGMENT_QLT);
lclr = fr.gkFragment_getClearRegionBegin(clrToDump) + 1;
rclr = fr.gkFragment_getClearRegionEnd (clrToDump);
seq = fr.gkFragment_getSequence() + ((dumpAllBases == false) ? fr.gkFragment_getClearRegionBegin(clrToDump) : 0);
qlt = fr.gkFragment_getQuality() + ((dumpAllBases == false) ? fr.gkFragment_getClearRegionBegin(clrToDump) : 0);
len = (dumpAllBases == false) ? fr.gkFragment_getClearRegionLength(clrToDump) : fr.gkFragment_getSequenceLength();
seq[len] = 0;
qlt[len] = 0;
// Write the second fragment (twice).
AS_UTL_writeFastQ(lib[libIID]->b, seq, len, qlt, len,
"@%s clr="F_U32","F_U32" clv="F_U32","F_U32" max="F_U32","F_U32" tnt="F_U32","F_U32" rnd=%c\n",
AS_UID_toString(fr.gkFragment_getReadUID()),
fr.gkFragment_getClearRegionBegin(clrToDump),
fr.gkFragment_getClearRegionEnd (clrToDump),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_TNT),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_TNT),
fr.gkFragment_getIsNonRandom() ? 'f' : 't');
AS_UTL_writeFastQ(lib[libIID]->p, seq, len, qlt, len,
"@%s clr="F_U32","F_U32" clv="F_U32","F_U32" max="F_U32","F_U32" tnt="F_U32","F_U32" rnd=%c\n",
AS_UID_toString(fr.gkFragment_getReadUID()),
fr.gkFragment_getClearRegionBegin(clrToDump),
fr.gkFragment_getClearRegionEnd (clrToDump),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_VEC),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_MAX),
fr.gkFragment_getClearRegionBegin(AS_READ_CLEAR_TNT),
fr.gkFragment_getClearRegionEnd (AS_READ_CLEAR_TNT),
fr.gkFragment_getIsNonRandom() ? 'f' : 't');
}
delete fs;
delete gkp;
exit(0);
}
