static rc_t bam_header(const VDatabase* db) {
rc_t rc = 0;
const char path[] = "BAM_HEADER";
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
char* buffer = NULL;
assert(db);
if (rc == 0) {
rc = VDatabaseOpenMetadataRead(db, &meta);
DISP_RC(rc, "while calling VDatabaseOpenMetadataRead");
}
if (rc == 0) {
rc = KMetadataOpenNodeRead(meta, &node, "%s", path);
if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
else {
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (rc == 0) {
int i = 0;
size_t bsize = 0;
size_t size = 1024;
for (i = 0; i < 2; ++i) {
free(buffer);
bsize = size + 1;
buffer = malloc(bsize);
if (buffer == NULL) {
rc = RC(rcExe, rcStorage, rcAllocating,
rcMemory, rcExhausted);
}
else {
rc = KMDataNodeReadCString(node, buffer, bsize, &size);
if (rc == 0) {
break;
}
else if (i == 0
&& GetRCObject(rc) == (enum RCObject)rcBuffer
&& GetRCState (rc) == rcInsufficient)
{
rc = 0;
}
}
DISP_RC2(rc, path, "while calling KMDataNodeReadCString");
}
}
}
}
if (rc == 0 && buffer)
{ OUTMSG(("BAM_HEADER: {\n%s}\n\n", buffer)); }
DESTRUCT(KMDataNode, node);
DESTRUCT(KMetadata, meta);
free(buffer);
return rc;
}
static rc_t align_info(const Params* prm) {
rc_t rc = 0;
const VDatabase* db = NULL;
const VDBManager* mgr = NULL;
const KDBManager *kmgr = NULL;
VSchema* schema = NULL;
bool is_db = false;
if (prm == NULL)
{ return RC(rcExe, rcQuery, rcExecuting, rcParam, rcNull); }
if (rc == 0) {
rc = VDBManagerMakeRead(&mgr, NULL);
DISP_RC(rc, "while calling VDBManagerMakeRead");
}
if (rc == 0) {
rc = VDBManagerOpenKDBManagerRead(mgr, &kmgr);
DISP_RC(rc, "while calling VDBManagerOpenKDBManagerRead");
}
if (rc == 0) {
rc = VDBManagerMakeSRASchema(mgr, &schema);
DISP_RC(rc, "while calling VDBManagerMakeSRASchema");
}
if (rc == 0) {
/* const char path[] = "/panfs/pan1/trace_work/scratch/XXX000013"; */
rc = VDBManagerOpenDBRead(mgr, &db, schema, prm->dbPath);
if (rc == 0) {
is_db = true;
}
else if (rc == SILENT_RC(rcDB, rcMgr, rcOpening, rcDatabase, rcIncorrect)) {
PLOGMSG(klogWarn, (klogWarn,
"'$(path)' is not a database", "path=%s", prm->dbPath));
rc = 0;
}
else {
PLOGERR(klogErr,
(klogErr, rc, "$(path)", "path=%s", prm->dbPath));
}
}
if (is_db) {
if (rc == 0) {
if (prm->paramRef) {
const VDBDependencies* dep = NULL;
uint32_t count = 0;
int i = 0;
rc = VDatabaseListDependencies(db, &dep, false);
DISP_RC2(rc, prm->dbPath,
"while calling VDatabaseListDependencies");
if (rc == 0) {
rc = VDBDependenciesCount(dep, &count);
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCount");
}
for (i = 0; i < count && rc == 0; ++i) {
bool circular = false;
const char* name = NULL;
const char* path = NULL;
const char* remote = NULL;
bool local = false;
const char* seqId = NULL;
rc = VDBDependenciesCircular(dep, &circular, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesCircular");
break;
}
rc = VDBDependenciesName(dep, &name, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesName");
break;
}
rc = VDBDependenciesPath(dep, &path, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesPath");
break;
}
rc = VDBDependenciesLocal(dep, &local, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesLocal");
break;
}
rc = VDBDependenciesSeqId(dep, &seqId, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesSeqId");
break;
}
rc = VDBDependenciesPathRemote(dep, &remote, i);
if (rc != 0) {
DISP_RC2(rc, prm->dbPath,
"while calling VDBDependenciesRemote");
break;
}
OUTMSG(("%s,%s,%s,%s", seqId, name,
(circular ? "true" : "false"),
(local ? "local" : "remote")));
if (path && path[0]) {
OUTMSG((":%s", path));
}
else if (remote && remote[0]) {
OUTMSG(("::%s", remote));
}
OUTMSG(("\n"));
}
DESTRUCT(VDBDependencies, dep);
}
if (prm->paramBamHeader) {
rc_t rc3 = bam_header(db);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
if (prm->paramQuality) {
rc_t rc3 = qual_stats(prm, db);
if (rc3 != 0 && rc == 0)
{ rc = rc3; }
}
}
}
DESTRUCT(VSchema, schema);
DESTRUCT(KDBManager, kmgr);
DESTRUCT(VDBManager, mgr);
DESTRUCT(VDatabase, db);
return rc;
}
static rc_t qual_stats(const Params* prm, const VDatabase* db) {
rc_t rc = 0;
const char tblName[] = "SEQUENCE";
const VTable* tbl = NULL;
const KMetadata* meta = NULL;
const KMDataNode* node = NULL;
assert(prm && db);
if (rc == 0) {
rc = VDatabaseOpenTableRead(db, &tbl, tblName);
DISP_RC2(rc, tblName, "while calling VDatabaseOpenTableRead");
}
if (rc == 0) {
rc = VTableOpenMetadataRead(tbl, &meta);
DISP_RC2(rc, tblName, "while calling VTableOpenMetadataRead");
}
if (rc == 0) {
bool found = false;
const char path[] = "STATS/QUALITY";
rc = KMetadataOpenNodeRead(meta, &node, path);
if (rc == 0)
{ found = true; }
else if (GetRCState(rc) == rcNotFound)
{ rc = 0; }
DISP_RC2(rc, path, "while calling KMetadataOpenNodeRead");
if (found) {
uint32_t i = 0;
int nbr = 0;
uint32_t count = 0;
KNamelist* names = NULL;
int* quals = NULL;
if (rc == 0) {
rc = KMDataNodeListChild(node, &names);
DISP_RC2(rc, path, "while calling KMDataNodeListChild");
}
if (rc == 0) {
rc = KNamelistCount(names, &count);
DISP_RC2(rc, path, "while calling KNamelistCount");
if (rc == 0 && count > 0) {
quals = calloc(count, sizeof *quals);
if (quals == NULL) {
rc = RC(rcExe,
rcStorage, rcAllocating, rcMemory, rcExhausted);
}
}
}
for (i = 0; i < count && rc == 0; ++i) {
/* uint64_t u = 0;
const KMDataNode* n = NULL; */
const char* nodeName = NULL;
const char* name = NULL;
rc = KNamelistGet(names, i, &nodeName);
DISP_RC2(rc, path, "while calling KNamelistGet");
if (rc)
{ break; }
name = nodeName;
/* rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
DISP_RC(rc, name);
} */
if (rc == 0) {
char* c = strchr(name, '_');
if (c != NULL && *(c + 1) != '\0') {
name = c + 1;
if (sscanf(name, "%d", &quals[i]) != 1) {
rc = RC(rcExe,
rcNode, rcParsing, rcName, rcUnexpected);
PLOGERR(klogInt,
(klogInt, rc, "$(name)", "name=%s", nodeName));
}
}
/* OUTMSG(("QUALITY %s %lu\n", name, u)); */
}
/* DESTRUCT(KMDataNode, n); */
}
if (rc == 0 && count > 0)
{ ksort(quals, count, sizeof *quals, sort_callback, NULL); }
if (rc == 0) {
OUTMSG(("%s", prm->dbPath));
}
for (i = 0, nbr = 0; i < count && rc == 0; ++i, ++nbr) {
uint64_t u = 0;
char name[64];
const KMDataNode* n = NULL;
sprintf(name, "PHRED_%d", quals[i]);
rc = KMDataNodeOpenNodeRead(node, &n, name);
DISP_RC(rc, name);
if (rc == 0) {
rc = KMDataNodeReadAsU64(n, &u);
DISP_RC(rc, name);
if (rc == 0) {
while (nbr < quals[i]) {
OUTMSG(("\t0"));
++nbr;
}
OUTMSG(("\t%lu", u));
/* OUTMSG(("QUALITY %d %lu\n", quals[i], u)); */
}
}
DESTRUCT(KMDataNode, n);
}
while (rc == 0 && nbr <= 40) {
OUTMSG(("\t0"));
nbr++;
}
if (rc == 0) {
OUTMSG(("\n"));
}
DESTRUCT(KNamelist, names);
}
}
DESTRUCT(KMDataNode, node);
DESTRUCT(KMetadata, meta);
DESTRUCT(VTable, tbl);
return rc;
}