int32
abAbacus::addContig() {
if (tigStore)
uma = tigStore->loadMultiAlign(iid, type == AS_UNITIG);
if (uma == NULL)
fprintf(stderr,"Lookup failure in CNS: MultiAlign for unitig %d could not be found.\n",iid);
assert(uma != NULL);
// Contigs used to be added gapped, unitigs as ungapped.
// This caused no end of trouble in MergeMultiAligns and
// ReplaceEndUnitigInContig.
ResetVA_char(ungappedSequence);
ResetVA_char(ungappedQuality);
GetMultiAlignUngappedConsensus(uma, ungappedSequence, ungappedQuality);
sequence = Getchar(ungappedSequence,0);
quality = Getchar(ungappedQuality,0);
fragment.length = GetMultiAlignUngappedLength(uma);
fragment.utype = (type == AS_UNITIG) ? utype : AS_OTHER_UNITIG;
fragment.n_components = GetNumIntMultiPoss(uma->f_list) + GetNumIntUnitigPoss(uma->u_list);
fragment.components = SetUngappedFragmentPositions(type, fragment.n_components, uma);
//fprintf(stderr, "AppendFragToLocalStore()-- TIG %d len=%d\n", iid, fragment.length);
}
int32
main(int32 argc, char **argv) {
int32 arg = 1;
int32 err = 0;
int32 hlp = 0;
char * gkpStoreName = NULL;
int32 gkpStorePart = 0;
char * msgFile = NULL;
char * outputFileName= NULL;
char * seqAn = NULL;
char * wrkDir = NULL;
char * seqStoreName = NULL;
int32 seqStoreVer = 0;
int32 seqStorePart = 0;
argc = AS_configure(argc, argv);
while (arg < argc) {
if (strcmp(argv[arg], "-c") == 0) {
msgFile = argv[++arg];
} else if (strcmp(argv[arg], "-G") == 0) {
gkpStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-S") == 0) {
gkpStorePart = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-o") == 0) {
outputFileName = argv[++arg];
} else if (strcmp(argv[arg], "-s") == 0) {
seqAn = argv[++arg];
} else if (strcmp(argv[arg], "-w") == 0) {
wrkDir = argv[++arg];
} else if (strcmp(argv[arg], "-u") == 0) {
seqStoreName = argv[++arg];
} else if (strcmp(argv[arg], "-V") == 0) {
seqStoreVer = atoi(argv[++arg]);
} else if (strcmp(argv[arg], "-p") == 0) {
seqStorePart = atoi(argv[++arg]);
} else {
err++;
}
arg++;
}
if ((err) || (gkpStoreName == NULL) || (msgFile == NULL) || (outputFileName == NULL) || seqAn == NULL) {
fprintf(stderr, "USAGE: SeqAn_CNS -G <gkpStore> -c <input.cgb> -o <output.cgi> -s <seqan_executable> [-u seqstore, required for contig consensus] [-w working directory]\n");
exit(1);
}
gkStore *gkpStore = new gkStore(gkpStoreName, FALSE, FALSE);
gkpStore->gkStore_loadPartition(gkpStorePart);
gkFragment fr;
GenericMesg *pmesg;
tSequenceDB *sequenceDB = NULL;
FILE *infp = fopen(msgFile,"r");
FILE *tempReads;
FILE *outfp = fopen(outputFileName, "w");
char fileName[AS_SEQAN_MAX_BUFFER_LENGTH];
char *prefix = outputFileName;
getFileName(prefix, wrkDir, AS_SEQAN_INPUT_NAME, fileName);
int32 i = 0;
while ((EOF != ReadProtoMesg_AS(infp, &pmesg))) {
int32 freeMem = 0;
if (pmesg->t == MESG_IUM) {
IntUnitigMesg *ium_mesg = (IntUnitigMesg *)pmesg->m;
if (strlen(ium_mesg->consensus) == 0) {
tempReads = fopen(fileName,"w");
for (i =0; i < ium_mesg->num_frags; i++) {
// get the fragment sequence
gkpStore->gkStore_getFragment(ium_mesg->f_list[i].ident, &fr, GKFRAGMENT_QLT);
uint32 clrBeg = fr.gkFragment_getClearRegionBegin();
uint32 clrEnd = fr.gkFragment_getClearRegionEnd ();
char *seqStart = fr.gkFragment_getSequence();
char *seq = seqStart+clrBeg;
seq[clrEnd] = 0;
AS_UTL_writeFastA(tempReads,
seq, clrEnd-clrBeg,
">"F_IID","F_IID"\n", ium_mesg->f_list[i].position.bgn, ium_mesg->f_list[i].position.end);
}
fclose(tempReads);
updateRecord(ium_mesg, fileName, seqAn, prefix, wrkDir);
freeMem = 1;
}
WriteProtoMesg_AS(outfp, pmesg);
if (freeMem) {
safe_free(ium_mesg->consensus);
safe_free(ium_mesg->quality);
}
}
else if (pmesg->t == MESG_ICM) {
IntConConMesg *icm_mesg = (IntConConMesg *)pmesg->m;
if (seqStoreName == NULL) {
fprintf(stderr, "USAGE: The -u option is required for contig consensus\n");
exit(1);
}
if (sequenceDB == NULL) {
sequenceDB = openSequenceDB(seqStoreName, FALSE, seqStoreVer);
openSequenceDBPartition(sequenceDB, seqStorePart);
}
if (strlen(icm_mesg->consensus) == 0) {
tempReads = fopen(fileName,"w");
for (i =0; i < icm_mesg->num_pieces; i++) {
// get the fragment sequence
gkpStore->gkStore_getFragment(icm_mesg->pieces[i].ident, &fr, GKFRAGMENT_QLT);
uint32 clrBeg = fr.gkFragment_getClearRegionBegin();
uint32 clrEnd = fr.gkFragment_getClearRegionEnd ();
char *seqStart = fr.gkFragment_getSequence();
char *seq = seqStart+clrBeg;
seq[clrEnd] = 0;
AS_UTL_writeFastA(tempReads,
seq, clrEnd-clrBeg,
">"F_IID","F_IID"\n", icm_mesg->pieces[i].position.bgn, icm_mesg->pieces[i].position.end);
}
// now handle the unitig messages
for (i =0; i < icm_mesg->num_unitigs; i++) {
VA_TYPE(char) *ungappedSequence = CreateVA_char(0);
VA_TYPE(char) *ungappedQuality = CreateVA_char(0);
MultiAlignT *uma = loadMultiAlignTFromSequenceDB(sequenceDB, icm_mesg->unitigs[i].ident, 1);
assert(uma != NULL);
GetMultiAlignUngappedConsensus(uma, ungappedSequence, ungappedQuality);
char * seq = Getchar(ungappedSequence,0);
AS_UTL_writeFastA(tempReads,
seq, strlen(seq),
">"F_IID","F_IID"\n", icm_mesg->unitigs[i].position.bgn, icm_mesg->unitigs[i].position.end);
}
fclose(tempReads);
updateICMRecord(icm_mesg, fileName, seqAn, prefix, wrkDir);
freeMem = 1;
}
WriteProtoMesg_AS(outfp, pmesg);
if (freeMem) {
safe_free(icm_mesg->consensus);
safe_free(icm_mesg->quality);
}
}
}
fclose(infp);
fclose(outfp);
return 0;
}
