static rc_t get_max_remove( const Args * args, uint64_t * max_rem )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPTION_MAXREM, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionCount( $(option) ) failed in $(func)", "option=%s,func=%s", OPTION_MAXREM, __func__ ) );
}
else if ( count > 0 )
{
const char * s = NULL;
rc = ArgsOptionValue( args, OPTION_MAXREM, 0, &s );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionValue( $(option), 0 ) failed in $(func)", "option=%s,func=%s", OPTION_MAXREM, __func__ ) );
}
else if ( s != NULL )
{
char *endp;
*max_rem = strtou64( s, &endp, 10 );
}
}
return rc;
}
static rc_t cg_dump_get_uint32t_option( Args * args, const char * name, uint32_t * value, bool * found )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, name, &count );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot detect count of $(name) option", "name=%s", name ) );
}
else
{
*found = ( count > 0 );
}
if ( rc == 0 && ( *found ) )
{
const char * s;
rc = ArgsOptionValue( args, name, 0, &s );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot detect value of $(name) option", "name=%s", name ) );
}
else
{
*value = atoi( s );
}
}
return rc;
}
rc_t get_ro( Args * args, const char * name, const int32_t ** RO, uint32_t * ro_count )
{
rc_t rc = ArgsOptionCount( args, name, ro_count );
*RO = NULL;
if ( ( rc == 0 )&&( *ro_count > 0 ) )
{
*RO = calloc( sizeof **RO, *ro_count );
if ( *RO == NULL )
rc = RC( rcApp, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
else
{
uint32_t i;
for ( i = 0; i < *ro_count && rc == 0; ++i )
{
const char * s;
rc = ArgsOptionValue( args, name, i, &s );
if ( rc == 0 )
{
((int32_t*)(*RO))[i] = atoi( s );
}
}
}
}
return rc;
}
rc_t init_ref_regions( BSTree * tree, Args * args )
{
uint32_t count;
rc_t rc;
BSTreeInit( tree );
rc = ArgsOptionCount( args, OPTION_REF, &count );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ArgsOptionCount() failed" );
}
else
{
uint32_t i;
for ( i = 0; i < count && rc == 0; ++i )
{
const char * s;
rc = ArgsOptionValue( args, OPTION_REF, i, &s );
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionValue() failed" );
else
rc = parse_and_add_region( tree, s );
}
}
return rc;
}
static rc_t gather_matepair_distances( Args * args, samdump_opts * opts )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPT_MATE_DIST, &count );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error counting comandline option '$(t)'", "t=%s", OPT_REGION ) );
}
else if ( count > 0 )
{
uint32_t i;
VectorInit( &opts->mp_dist, 0, 10 );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * s;
rc = ArgsOptionValue( args, OPT_MATE_DIST, i, &s );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)'", "t=%s", OPT_MATE_DIST ) );
}
else
rc = parse_and_add_matepair_dist( &opts->mp_dist, s );
}
opts->use_matepair_filter = ( VectorLength( &opts->mp_dist ) > 0 );
}
return rc;
}
static rc_t gather_region_options( Args * args, samdump_opts * opts )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPT_REGION, &count );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error counting comandline option '$(t)'", "t=%s", OPT_REGION ) );
}
else if ( count > 0 )
{
uint32_t i;
BSTreeInit( &opts->regions );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * s;
rc = ArgsOptionValue( args, OPT_REGION, i, &s );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)'", "t=%s", OPT_REGION ) );
}
else
rc = parse_and_add_region( &opts->regions, s );
}
if ( rc == 0 )
{
check_ref_regions( &opts->regions );
opts->region_count = count_ref_regions( &opts->regions );
}
}
return rc;
}
static KRepCategory get_repo_select( const Args * args, const char * name )
{
KRepCategory res = krepBadCategory;
uint32_t count;
rc_t rc = ArgsOptionCount( args, name, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionCount() failed in $(func)", "func=%s", __func__ ) );
}
else if ( count > 0 )
{
const char * s = NULL;
rc = ArgsOptionValue( args, name, 0, &s );
if ( rc == 0 && s != NULL )
{
if ( string_cmp_1 ( s, "user" ) )
res = krepUserCategory;
else if ( string_cmp_1 ( s, "site" ) )
res = krepSiteCategory;
else if ( string_cmp_1 ( s, "rem" ) )
res = krepRemoteCategory;
}
}
return res;
}
static
uint64_t ArgsGetOptU64 ( Args *self, const ctx_t *ctx, const char *optname, uint32_t *count )
{
rc_t rc;
uint64_t val = 0;
uint32_t dummy;
if ( count == NULL )
count = & dummy;
rc = ArgsOptionCount ( self, optname, count );
if ( rc == 0 && * count != 0 )
{
const char *str;
rc = ArgsOptionValue ( self, optname, 0, & str );
if ( rc != 0 )
INTERNAL_ERROR ( rc, "failed to retrieve '%s' parameter", optname );
else
{
char *end;
val = strtou64 ( str, & end, 0 );
if ( end [ 0 ] != 0 )
{
rc = RC ( rcExe, rcArgv, rcParsing, rcParam, rcIncorrect );
ERROR ( rc, "bad '%s' parameter: '%s'", optname, str );
}
}
}
return val;
}
static rc_t getArgValue(Args *const args, char const *name, int index, char const **result)
{
void const *value;
rc_t const rc = ArgsOptionValue(args, name, index, &value);
if (rc) return rc;
free((void *)*result);
*result = strdup(value);
assert(*result);
return 0;
}
static rc_t get_str_option( const Args * args, const char * option_name, const char ** dst, const char * default_value )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, option_name, &count );
if ( ( rc == 0 )&&( count > 0 ) )
rc = ArgsOptionValue( args, option_name, 0, (const void **)dst );
else
(*dst) = string_dup_measure ( default_value, NULL );
return rc;
}
static const char* get_str_option( const Args *my_args, const char *name )
{
const char* res = NULL;
uint32_t count;
rc_t rc = ArgsOptionCount( my_args, name, &count );
if ( ( rc == 0 )&&( count > 0 ) )
{
ArgsOptionValue( my_args, name, 0, (const void **)&res );
}
return res;
}
LIB_EXPORT rc_t CC XMLLogger_Make(const XMLLogger** cself, KDirectory* dir, const Args *args)
{
rc_t rc = 0;
const char* path = NULL, *sfd = NULL;
int fd = -1;
uint32_t count;
if( (rc = ArgsOptionCount(args, XMLLogger_Args[eopt_file].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcApp, rcArgv, rcParsing, rcParam, rcExcessive);
} else if( count > 0 && (rc = ArgsOptionValue(args, XMLLogger_Args[eopt_file].name, 0, (const void **)&path)) != 0 ) {
} else if( (rc = ArgsOptionCount(args, XMLLogger_Args[eopt_fd].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcApp, rcArgv, rcParsing, rcParam, rcExcessive);
} else if( count > 0 && (rc = ArgsOptionValue(args, XMLLogger_Args[eopt_fd].name, 0, (const void **)&sfd)) != 0 ) {
} else {
do {
long val = 0;
char* end = NULL;
if( sfd != NULL ) {
if( path != NULL ) {
rc = RC(rcApp, rcArgv, rcParsing, rcParam, rcExcessive);
break;
}
errno = 0;
val = strtol(sfd, &end, 10);
if( errno != 0 || sfd == end || *end != '\0' || val < 0 || val > INT_MAX ) {
rc = RC(rcApp, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
fd = val;
}
rc = XMLLogger_Make2(cself, dir, path, fd);
} while( false );
}
return rc;
}
static uint32_t get_uint32_option( const Args *my_args,
const char *name,
const uint32_t def )
{
uint32_t count, res = def;
rc_t rc = ArgsOptionCount( my_args, name, &count );
if ( ( rc == 0 )&&( count > 0 ) )
{
const char *s;
rc = ArgsOptionValue( my_args, name, 0, &s );
if ( rc == 0 ) res = strtoul( s, NULL, 10 );
}
return res;
}
static void append_str_options( const Args *my_args, const char *name, VNamelist *dst )
{
uint32_t count;
rc_t rc = ArgsOptionCount( my_args, name, &count );
if ( ( rc == 0 )&&( count > 0 ) )
{
uint32_t idx;
for ( idx=0; idx<count; ++idx )
{
const char* s;
if ( ArgsOptionValue( my_args, name, idx, (const void **)&s ) == 0 )
VNamelistAppend( dst, s );
}
}
}
static
const char *ArgsGetOptStr ( Args *self, const ctx_t *ctx, const char *optname, uint32_t *count )
{
rc_t rc;
const char *val = NULL;
uint32_t dummy;
if ( count == NULL )
count = & dummy;
rc = ArgsOptionCount ( self, optname, count );
if ( rc == 0 && * count != 0 )
{
rc = ArgsOptionValue ( self, optname, 0, & val );
if ( rc != 0 )
INTERNAL_ERROR ( rc, "failed to retrieve '%s' parameter", optname );
}
return val;
}
rc_t get_str_option( const Args *args, const char *name, const char ** res )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, name, &count );
*res = NULL;
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionCount() failed" );
else
{
if ( count > 0 )
{
rc = ArgsOptionValue( args, name, 0, res );
if ( rc != 0 )
{
LOGERR( klogInt, rc, "ArgsOptionValue() failed" );
}
}
}
return rc;
}
static rc_t get_str_option( Args * args, const char * name, const char ** s )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, name, &count );
*s = NULL;
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error counting comandline option '$(t)'", "t=%s", name ) );
}
else if ( count > 0 )
{
rc = ArgsOptionValue( args, name, 0, s );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)'", "t=%s", name ) );
}
}
return rc;
}
rc_t get_uint32_array( const Args *args, const char *name,
uint32_t *res, uint32_t *count )
{
uint32_t max = *count;
rc_t rc = ArgsOptionCount( args, name, count );
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionCount() failed" );
else
{
uint32_t i;
if ( *count > max ) *count = max;
for ( i = 0; i < *count && rc == 0; ++ i )
{
const char * s;
rc = ArgsOptionValue( args, name, i, &s );
if ( rc == 0 )
*(res++) = atoi( s );
}
}
return rc;
}
rc_t get_slices( const Args * args, const char *option, Vector * slices )
{
uint32_t count, i;
rc_t rc = ArgsOptionCount( args, option, &count );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * value;
rc = ArgsOptionValue( args, option, i, ( const void ** )&value );
if ( rc == 0 && value != NULL )
{
String S;
StringInitCString( &S, value );
{
slice * s = make_slice_from_str( &S );
rc = VectorAppend( slices, NULL, s );
if ( rc != 0 )
release_slice( s );
}
}
}
return rc;
}
rc_t CC Args_parse_inf_file( Args * args, const char * file_option )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, file_option, &count );
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionCount() failed" );
else if ( count > 0 )
{
uint32_t count2 = 0;
do
{
uint32_t idx;
for ( idx = count2; idx < count && rc == 0; ++idx )
{
const char *filename;
rc = ArgsOptionValue( args, file_option, idx, (const void **)&filename );
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionValue() failed" );
else if ( filename != NULL )
{
int argc;
char ** argv;
rc = Args_tokenize_file_into_argv( filename, &argc, &argv );
if ( rc == 0 && argv != NULL && argc > 0 )
{
rc = ArgsParse ( args, argc, argv );
Args_free_token_argv( argc, argv );
}
}
}
count2 = count;
rc = ArgsOptionCount( args, file_option, &count );
if ( rc != 0 )
LOGERR( klogInt, rc, "ArgsOptionCount() failed" );
} while ( rc == 0 && count > count2 );
}
return rc;
}
static rc_t get_user_repo_name( const Args * args, const char ** name )
{
uint32_t count;
rc_t rc = ArgsOptionCount( args, OPTION_URNAME, &count );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionCount( $(option) ) failed in $(func)", "option=%s,func=%s", OPTION_URNAME, __func__ ) );
}
else if ( count > 0 )
{
const char * s = NULL;
rc = ArgsOptionValue( args, OPTION_URNAME, 0, &s );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"ArgsOptionValue( $(option), 0 ) failed in $(func)", "option=%s,func=%s", OPTION_URNAME, __func__ ) );
}
else if ( s != NULL )
*name = string_dup_measure ( s, NULL );
}
return rc;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
rc_t rc;
unsigned n_aligned = 0;
unsigned n_unalgnd = 0;
char *aligned[256];
char *unalgnd[256];
char *name_buffer = NULL;
unsigned next_name = 0;
unsigned nbsz = 0;
char const *value;
char *dummy;
const XMLLogger* xml_logger = NULL;
memset(&G, 0, sizeof(G));
G.mode = mode_Archive;
G.maxSeqLen = TableWriterRefSeq_MAX_SEQ_LEN;
G.schemaPath = SCHEMAFILE;
G.omit_aligned_reads = true;
G.omit_reference_reads = true;
G.minMapQual = 0; /* accept all */
G.tmpfs = "/tmp";
#if _ARCH_BITS == 32
G.cache_size = ( size_t ) 1 << 30;
#else
G.cache_size = ( size_t ) 10 << 30;
#endif
G.maxErrCount = 1000;
G.minMatchCount = 10;
set_pid();
rc = ArgsMakeAndHandle (&args, argc, argv, 2, Options,
sizeof Options / sizeof (OptDef), XMLLogger_Args, XMLLogger_ArgsQty);
while (rc == 0) {
uint32_t pcount;
if( (rc = XMLLogger_Make(&xml_logger, NULL, args)) != 0 ) {
break;
}
rc = ArgsOptionCount(args, option_only_verify, &pcount);
if (rc)
break;
G.onlyVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_no_verify, &pcount);
if (rc)
break;
G.noVerifyReferences = (pcount > 0);
rc = ArgsOptionCount(args, option_use_qual, &pcount);
if (rc)
break;
G.useQUAL = (pcount > 0);
rc = ArgsOptionCount(args, option_ref_config, &pcount);
if (rc)
break;
G.limit2config = (pcount > 0);
rc = ArgsOptionCount(args, OPTION_REF_FILE, &pcount);
if (rc)
break;
G.refFiles = calloc(pcount + 1, sizeof(*(G.refFiles)));
if( !G.refFiles ) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
while(pcount-- > 0) {
rc = ArgsOptionValue(args, OPTION_REF_FILE, pcount, &G.refFiles[pcount]);
if (rc)
break;
}
rc = ArgsOptionCount (args, OPTION_TMPFS, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_TMPFS, 0, &G.tmpfs);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_INPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_INPUT, 0, &G.inpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, option_ref_filter, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_ref_filter, 0, &G.refFilter);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_CONFIG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CONFIG, 0, &G.refXRefPath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single input parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_OUTPUT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_OUTPUT, 0, &G.outpath);
if (rc)
break;
}
else if (pcount > 1)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
OUTMSG (("Single output parameter required\n"));
MiniUsage (args);
break;
}
else if (!G.onlyVerifyReferences) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
OUTMSG (("Output parameter required\n"));
MiniUsage (args);
break;
}
rc = ArgsOptionCount (args, OPTION_MINMAPQ, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MINMAPQ, 0, &value);
if (rc)
break;
G.minMapQual = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_QCOMP, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_QCOMP, 0, &G.QualQuantizer);
if (rc)
break;
}
rc = ArgsOptionCount (args, option_edit_aligned_qual, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, option_edit_aligned_qual, 0, &value);
if (rc)
break;
G.alignedQualValue = strtoul(value, &dummy, 0);
if (G.alignedQualValue == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("edit-aligned-qual: bad value\n"));
MiniUsage (args);
break;
}
G.editAlignedQual = true;
}
rc = ArgsOptionCount (args, OPTION_CACHE_SIZE, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_CACHE_SIZE, 0, &value);
if (rc)
break;
G.cache_size = strtoul(value, &dummy, 0) * 1024UL * 1024UL;
if (G.cache_size == 0) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcIncorrect);
OUTMSG (("cache-size: bad value\n"));
MiniUsage (args);
break;
}
}
rc = ArgsOptionCount (args, OPTION_MAX_WARN_DUP_FLAG, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_WARN_DUP_FLAG, 0, &value);
if (rc)
break;
G.maxWarnCount_DupConflict = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, option_unsorted, &pcount);
if (rc)
break;
G.expectUnsorted = pcount > 0;
rc = ArgsOptionCount (args, OPTION_MAX_REC_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_REC_COUNT, 0, &value);
if (rc)
break;
G.maxAlignCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MAX_ERR_COUNT, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MAX_ERR_COUNT, 0, &value);
if (rc)
break;
G.maxErrCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_MIN_MATCH, &pcount);
if (rc)
break;
if (pcount == 1)
{
rc = ArgsOptionValue (args, OPTION_MIN_MATCH, 0, &value);
if (rc)
break;
G.minMatchCount = strtoul(value, &dummy, 0);
}
rc = ArgsOptionCount (args, OPTION_ACCEPT_DUP, &pcount);
if (rc)
break;
G.acceptBadDups = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_NOMATCH, &pcount);
if (rc)
break;
G.acceptNoMatch = pcount > 0;
rc = ArgsOptionCount (args, option_keep_mismatch_qual, &pcount);
if (rc)
break;
G.keepMismatchQual = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_CS, &pcount);
if (rc)
break;
G.noColorSpace = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NO_SECONDARY, &pcount);
if (rc)
break;
G.noSecondary = pcount > 0;
rc = ArgsOptionCount (args, OPTION_TI, &pcount);
if (rc)
break;
G.hasTI = pcount > 0;
rc = ArgsOptionCount (args, OPTION_ACCEPT_HARD_CLIP, &pcount);
if (rc)
break;
G.acceptHardClip = pcount > 0;
rc = ArgsOptionCount (args, OPTION_NOMATCH_LOG, &pcount);
if (rc)
break;
if (pcount == 1)
{
KDirectory *dir;
rc = ArgsOptionValue (args, OPTION_NOMATCH_LOG, 0, &value);
if (rc) break;
rc = KDirectoryNativeDir(&dir);
if (rc) break;
rc = KDirectoryCreateFile(dir, &G.noMatchLog, 0, 0664, kcmInit, value);
KDirectoryRelease(dir);
if (rc) break;
}
rc = ArgsOptionCount (args, OPTION_HEADER, &pcount);
if (rc)
break;
if (pcount == 1) {
rc = ArgsOptionValue (args, OPTION_HEADER, 0, &value);
if (rc) break;
rc = LoadHeader(&G.headerText, value, G.inpath);
if (rc) break;
}
rc = ArgsParamCount (args, &pcount);
if (rc) break;
if (pcount == 0)
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcInsufficient);
MiniUsage (args);
break;
}
else if (pcount > sizeof(aligned)/sizeof(aligned[0])) {
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
(void)PLOGERR(klogErr, (klogErr, rc, "$(count) input files is too many, $(max) is the limit",
"count=%u,max=%u", (unsigned)pcount, (unsigned)(sizeof(aligned)/sizeof(aligned[0]))));
break;
}
else {
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
nbsz = need;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc)
break;
if (pcount > 0)
{
unsigned need = G.inpath ? (strlen(G.inpath) + 1) * pcount : 0;
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
need += strlen(value) + 1;
}
if (rc) break;
nbsz += need;
}
name_buffer = malloc(nbsz);
if (name_buffer == NULL) {
rc = RC(rcApp, rcArgv, rcAccessing, rcMemory, rcExhausted);
break;
}
rc = ArgsOptionCount (args, OPTION_UNALIGNED, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsOptionValue(args, OPTION_UNALIGNED, i, &value);
if (rc) break;
unalgnd[n_unalgnd++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
if (rc) break;
}
else
break;
rc = ArgsParamCount (args, &pcount);
if (rc == 0) {
unsigned i;
for (i = 0; i < pcount; ++i) {
rc = ArgsParamValue(args, i, &value);
if (rc) break;
aligned[n_aligned++] = name_buffer + next_name;
rc = PathWithBasePath(name_buffer + next_name, nbsz - next_name, value, G.inpath);
if (rc) break;
next_name += strlen(name_buffer + next_name) + 1;
}
}
else
break;
rc = run(argv[0], n_aligned, (char const **)aligned, n_unalgnd, (char const **)unalgnd);
break;
}
free(name_buffer);
free((void *)G.headerText);
free(G.refFiles);
value = G.outpath ? strrchr(G.outpath, '/') : "/???";
if( value == NULL ) {
value = G.outpath;
} else {
value++;
}
if (rc) {
(void)PLOGERR(klogErr, (klogErr, rc, "load failed",
"severity=total,status=failure,accession=%s,errors=%u", value, G.errCount));
} else {
(void)PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s,errors=%u", value, G.errCount));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1, MyOptions, sizeof MyOptions / sizeof (OptDef));
if (rc)
LOGERR (klogInt, rc, "failed to parse arguments");
else
{
do
{
KDyld *dl;
uint32_t num_libs;
rc = ArgsParamCount (args, &num_libs);
if (rc)
{
LOGERR ( klogInt, rc, "Failure to count parameters" );
break;
}
if (num_libs == 0)
{
rc = MiniUsage(args);
break;
}
/* create loader */
rc = KDyldMake (&dl);
if (rc)
{
LOGERR ( klogInt, rc, "failed to create dynamic loader" );
break;
}
else
{
do
{
KDlset *libs;
const char * path;
uint32_t ix;
uint32_t num_paths;
rc = ArgsOptionCount (args, OPTION_LOAD, &num_paths);
if (rc)
{
LOGERR (klogInt, rc, "failed to count paths");
break;
}
for (ix = 0; ix < num_paths; ix++)
{
rc = ArgsOptionValue (args, OPTION_LOAD, ix, (const void **)&path);
if (rc)
{
LOGERR (klogInt, rc, "failed to access a path option");
break;
}
testld_update_libpath (dl, path);
}
if (rc)
break;
/* append contents of LD_LIBRARY_PATH */
path = getenv ( "LD_LIBRARY_PATH" );
if (path)
testld_update_libpath (dl, path);
/* create libset */
rc = KDyldMakeSet (dl, & libs);
if (rc)
{
LOGERR (klogInt, rc, "failed to create dl library set");
break;
}
else
{
/* test it */
for (ix = 0; ix < num_libs; ++ ix )
{
rc = ArgsParamValue (args, ix, (const void **)&path);
if (rc)
break;
testld_load_library (dl, libs, path);
}
KDlsetRelease ( libs );
}
} while (0);
KDyldRelease ( dl );
}
} while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv[] )
{
rc_t rc = 0;
Args * args;
rc = ArgsMakeStandardOptions (&args);
if (rc == 0)
{
do
{
uint32_t pcount;
rc = ArgsAddOptionArray (args, MyOptions, sizeof MyOptions / sizeof (OptDef));
if (rc)
break;
rc = ArgsParse (args, argc, argv);
if (rc)
break;
/* quirky way default path is generated means this comes
* before standard argument handling */
rc = ArgsOptionCount (args, OPTION_TABLE, &pcount);
if (rc)
break;
if (pcount == 0)
{
static char * default_name = "RowWriteTestOutTable";
char * user;
user = getenv ("USER");
if (user)
snprintf (tablePath, sizeof (tablePath),
"/home/%s/%s", user, default_name);
else
strncpy (tablePath, default_name, sizeof (tablePath));
}
else
{
const char * pc;
ArgsOptionValue (args, OPTION_TABLE, 0, &pc);
strncpy (tablePath, pc, sizeof (tablePath));
}
rc = ArgsHandleStandardOptions (args);
if (rc)
break;
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
if (pcount)
{
const char * pc;
rc = ArgsArgvValue (args, 0, &pc);
if (rc)
break;
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcExcessive);
PLOGERR (klogFatal, (klogFatal, rc, "$(P) takes no parameters", PLOG_S(P), pc));
break;
}
rc = ArgsOptionCount (args, OPTION_ROW, &pcount);
if (rc == 0)
{
uint64_t row_count;
if (pcount)
{
const char * pc;
rc = ArgsOptionValue (args, OPTION_ROW, 0, &pc);
if (rc)
break;
row_count = AsciiToU32 (pc, NULL, NULL);
}
else
row_count = ROWS;
rc = run (tablePath, row_count);
}
} while (0);
ArgsWhack (args);
}
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args *args;
rc_t rc;
do {
uint32_t paramc;
bool requireAmd64 = false;
uint64_t requireRam = 0;
rc = ArgsMakeAndHandle ( & args, argc, argv, 1,
Options, sizeof Options / sizeof (OptDef) );
if ( rc != 0 )
{
LogErr ( klogErr, rc, "failed to parse arguments" );
break;
}
// TODO: cehck if we need it
rc = ArgsParamCount ( args, & paramc );
if ( rc != 0 ) {
LogErr ( klogInt, rc, "failed to obtain param count" );
break;
}
{ // OPTION_AMD64
rc = ArgsOptionCount( args, OPTION_AMD64, & paramc );
if ( rc ) {
LOGERR( klogErr, rc, "Failure to get '" OPTION_AMD64 "' argument" );
break;
}
if ( paramc ) {
requireAmd64 = true;
}
}
{
// OPTION_RAM
rc = ArgsOptionCount ( args, OPTION_RAM, & paramc );
if ( rc ) {
LOGERR ( klogErr, rc, "Failure to get '" OPTION_RAM "' argument" );
break;
}
if ( paramc ) {
const char* dummy = NULL;
rc = ArgsOptionValue(args, OPTION_RAM, 0, (const void **)&dummy);
if ( rc ) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_RAM "' argument");
break;
}
rc = sscanf(dummy, "%llu", &requireRam);
if ( rc != 1)
{
LOGMSG(klogErr, "Failure to parse '" OPTION_RAM "' argument value");
break;
}
}
}
{
rc = KAppCheckEnvironment(requireAmd64, requireRam);
if (rc != 0 )
printf("Invalid environment\n");
else
printf("Enviroment is fine!\n");
}
} while (false);
ArgsWhack ( args );
return rc;
}
rc_t CC KMain( int argc, char *argv [] )
{
Args * args;
rc_t rc = ArgsMakeAndHandle( &args, argc, argv, 1, options, sizeof options / sizeof options [ 0 ] );
if ( rc == 0 )
{
try
{
NGS_Pileup::Settings settings;
uint32_t pcount;
rc = ArgsOptionCount ( args, OPTION_REF, &pcount );
if ( pcount > 1 )
{
throw ngs :: ErrorMsg ( "multiple positions are not supported at this point" );
}
if ( pcount == 1 )
{
const void * value;
rc = ArgsOptionValue ( args, OPTION_REF, 0, & value );
if ( rc != 0 )
{
throw ngs :: ErrorMsg ( "ArgsOptionValue (" OPTION_REF ") failed" );
}
settings . AddReference ( static_cast <char const*> (value) );
}
rc = ArgsParamCount ( args, &pcount );
if ( rc == 0 )
{
if ( pcount > 1 )
{
throw ngs :: ErrorMsg ( "multiple accessions are not supported at this point" );
}
settings . output = & std::cout;
void const *value;
rc = ArgsParamValue ( args, 0, &value );
if ( rc == 0 )
{
settings . AddInput ( static_cast <char const*> (value) );
NGS_Pileup ( settings ) . Run ();
}
else
{
throw ngs :: ErrorMsg ( "ArgsParamValue failed" );
}
}
}
catch (ngs :: ErrorMsg& ex)
{
std :: cerr << "Program aborted: " << ex.what() << std::endl;
exit ( -1 );
}
ArgsWhack( args );
}
return 0;
}
rc_t CC KMain (int argc, char * argv[])
{
Args * args;
uint32_t pcount;
rc_t rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if ( rc == 0 )
{
rc = ArgsParamCount (args, &pcount);
if ( rc == 0 )
{
if ( pcount != 0 )
{
rc = RC(rcApp, rcArgv, rcAccessing, rcParam, rcExcessive);
MiniUsage (args);
}
else
{
const KStream *std_in;
rc = KStreamMakeStdIn ( & std_in );
if ( rc == 0 )
{
KStream* buffered;
rc = KStreamMakeBuffered ( &buffered, std_in, 0 /*input-only*/, 0 /*use default size*/ );
if ( rc == 0 )
{
GeneralLoader loader ( *buffered );
rc = ArgsOptionCount (args, OPTION_INCLUDE_PATHS, &pcount);
if ( rc == 0 )
{
for ( uint32_t i = 0 ; i < pcount; ++i )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_INCLUDE_PATHS, i, &value);
if ( rc != 0 )
{
break;
}
loader . AddSchemaIncludePath ( value );
}
}
rc = ArgsOptionCount (args, OPTION_SCHEMAS, &pcount);
if ( rc == 0 )
{
for ( uint32_t i = 0 ; i < pcount; ++i )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_SCHEMAS, i, &value);
if ( rc != 0 )
{
break;
}
loader . AddSchemaFile( value );
}
}
rc = ArgsOptionCount (args, OPTION_TARGET, &pcount);
if ( rc == 0 && pcount == 1 )
{
const char* value;
rc = ArgsOptionValue (args, OPTION_TARGET, 0, &value);
if ( rc == 0 )
{
loader . SetTargetOverride ( value );
}
}
if ( rc == 0 )
{
rc = loader . Run();
}
KStreamRelease ( buffered );
}
KStreamRelease ( std_in );
}
}
}
}
if ( rc != 0)
{
LOGERR ( klogErr, rc, "load failed" );
}
ArgsWhack(args);
return rc;
}
rc_t CC KMain( int argc, char* argv[] )
{
rc_t rc = 0;
Args* args = NULL;
const char* errmsg = NULL, *refseq_chunk = NULL, *min_mapq = NULL, *cluster_size = NULL;
const XMLLogger* xml_logger = NULL;
SParam params;
memset(¶ms, 0, sizeof(params));
params.schema = "align/align.vschema";
params.argv0 = argv[0];
if( (rc = ArgsMakeAndHandle(&args, argc, argv, 2, MainArgs, MainArgsQty, XMLLogger_Args, XMLLogger_ArgsQty)) == 0 ) {
uint32_t count;
if( (rc = ArgsParamCount (args, &count)) != 0 || count != 0 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
ArgsParamValue(args, 0, &errmsg);
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Output].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_Output].name, 0, ¶ms.out)) != 0 ) {
errmsg = MainArgs[eopt_Output].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MapInput].name, &count)) != 0 || count != 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionValue(args, MainArgs[eopt_MapInput].name, 0, ¶ms.map_path)) != 0 ) {
errmsg = MainArgs[eopt_MapInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Schema].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, count ? rcExcessive : rcInsufficient);
errmsg = MainArgs[eopt_Schema].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Schema].name, 0, ¶ms.schema)) != 0 ) {
errmsg = MainArgs[eopt_Schema].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_AsmInput].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_AsmInput].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_AsmInput].name, 0, ¶ms.asm_path)) != 0 ) {
errmsg = MainArgs[eopt_AsmInput].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqConfig].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqConfig].name, 0, ¶ms.refseqcfg)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqConfig].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqPath].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqPath].name, 0, ¶ms.refseqpath)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqPath].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Library].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_Library].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_Library].name, 0, ¶ms.library)) != 0 ) {
errmsg = MainArgs[eopt_Library].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefSeqChunk].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_RefSeqChunk].name, 0, &refseq_chunk)) != 0 ) {
errmsg = MainArgs[eopt_RefSeqChunk].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_Force].name, ¶ms.force)) != 0 ) {
errmsg = MainArgs[eopt_Force].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRef].name, ¶ms.force_refw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRef].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ForceRead].name, ¶ms.force_readw)) != 0 ) {
errmsg = MainArgs[eopt_ForceRead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_noReadAhead].name, ¶ms.no_read_ahead)) != 0 ) {
errmsg = MainArgs[eopt_noReadAhead].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_NoSpotGroup].name, ¶ms.no_spot_group)) != 0 ) {
errmsg = MainArgs[eopt_NoSpotGroup].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_No2nd_ary].name, ¶ms.min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_No2nd_ary].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_QualQuantization].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_QualQuantization].name, 0, ¶ms.qual_quant)) != 0 ) {
errmsg = MainArgs[eopt_QualQuantization].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_MinMapQ].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_MinMapQ].name, 0, &min_mapq)) != 0 ) {
errmsg = MainArgs[eopt_MinMapQ].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_ClusterSize].name, &count)) != 0 || count > 1 ) {
rc = rc ? rc : RC(rcExe, rcArgv, rcParsing, rcParam, rcExcessive);
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( count > 0 && (rc = ArgsOptionValue(args, MainArgs[eopt_ClusterSize].name, 0, &cluster_size)) != 0 ) {
errmsg = MainArgs[eopt_ClusterSize].name;
} else if( (rc = ArgsOptionCount(args, MainArgs[eopt_SingleMate].name, ¶ms.single_mate)) != 0 ) {
errmsg = MainArgs[eopt_SingleMate].name;
} else {
do {
long val = 0;
char* end = NULL;
uint32_t count;
if( (rc = ArgsOptionCount(args, MainArgs[eopt_RefFile].name, &count)) != 0 ) {
break;
} else {
params.refFiles = calloc(count + 1, sizeof(*(params.refFiles)));
if( params.refFiles == NULL ) {
rc = RC(rcApp, rcArgv, rcReading, rcMemory, rcExhausted);
break;
}
while(rc == 0 && count-- > 0) {
rc = ArgsOptionValue(args, MainArgs[eopt_RefFile].name, count, ¶ms.refFiles[count]);
}
}
if( refseq_chunk != NULL ) {
errno = 0;
val = strtol(refseq_chunk, &end, 10);
if( errno != 0 || refseq_chunk == end || *end != '\0' || val < 0 || val > UINT32_MAX ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.refseq_chunk = val;
}
if( params.min_mapq > 0 ) {
params.min_mapq = ~0;
} else if( min_mapq != NULL ) {
errno = 0;
val = strtol(min_mapq, &end, 10);
if( errno != 0 || min_mapq == end || *end != '\0' || val < 0 || val > 255 ) {
rc = RC(rcExe, rcArgv, rcReading, rcParam, rcInvalid);
break;
}
params.min_mapq = val;
}
if ( cluster_size )
params.cluster_size = atoi( cluster_size );
else
params.cluster_size = 0;
rc = KDirectoryNativeDir( ¶ms.input_dir );
if ( rc != 0 )
errmsg = "current directory";
else
{
rc = XMLLogger_Make( &xml_logger, params.input_dir, args );
if ( rc != 0 )
errmsg = "XML logging";
else
rc = Load( ¶ms );
}
} while( false );
KDirectoryRelease( params.input_dir );
}
}
/* find accession as last part of path for internal XML logging */
refseq_chunk = params.out ? strrchr(params.out, '/') : "/???";
if( refseq_chunk ++ == NULL )
refseq_chunk = params.out;
if( argc < 2 )
MiniUsage(args);
else if( rc != 0 )
{
if( errmsg )
{
MiniUsage(args);
LOGERR(klogErr, rc, errmsg);
}
else
{
PLOGERR(klogErr, (klogErr, rc, "load failed: $(reason_short)",
"severity=total,status=failure,accession=%s", refseq_chunk));
}
}
else
{
PLOGMSG(klogInfo, (klogInfo, "loaded",
"severity=total,status=success,accession=%s", refseq_chunk));
}
ArgsWhack(args);
XMLLogger_Release(xml_logger);
return rc;
}
static rc_t ParamsConstruct(int argc, char* argv[], Params* prm) {
rc_t rc = 0;
Args* args = NULL;
int count = 0;
assert(argc && argv && prm);
memset(prm, 0, sizeof *prm);
args = prm->args;
do {
uint32_t pcount = 0;
rc = ArgsMakeAndHandle(&args, argc, argv, 1,
Options, sizeof Options / sizeof (OptDef));
if (rc) {
LOGERR(klogErr, rc, "While calling ArgsMakeAndHandle");
break;
}
prm->args = args;
rc = ArgsParamCount(args, &prm->argsParamCnt);
if (rc) {
LOGERR(klogErr, rc, "Failure to get query parameter[s]");
break;
}
if (prm->argsParamCnt > 0) {
prm->modeShowCfg = true;
++count;
}
prm->xml = true;
rc = ArgsOptionCount(args, OPTION_OUT, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_OUT "' argument");
break;
}
if (pcount) {
const char* dummy = NULL;
rc = ArgsOptionValue(args, OPTION_OUT, 0, &dummy);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_OUT "' argument");
break;
}
if (!strcmp(dummy, "n")) {
prm->xml = false;
}
else if (strcmp(dummy, "x")) {
rc = RC(rcExe, rcArgv, rcParsing, rcParam, rcInvalid);
LOGERR(klogErr, rc, "Bad " OPTION_OUT " value");
break;
}
}
rc = ArgsOptionCount(args, OPTION_CFG, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_CFG "' argument");
break;
}
if (pcount) {
if (!prm->modeShowCfg) {
prm->modeShowCfg = true;
++count;
}
}
rc = ArgsOptionCount(args, OPTION_ENV, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_ENV "' argument");
break;
}
if (pcount) {
prm->modeShowEnv = true;
++count;
}
rc = ArgsOptionCount(args, OPTION_FIL, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_FIL "' argument");
break;
}
if (pcount) {
prm->modeShowFiles = true;
++count;
}
rc = ArgsOptionCount(args, OPTION_IMP, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_IMP "' argument");
break;
}
if (pcount) {
rc = ArgsOptionValue(args, OPTION_IMP, 0, &prm->ngc);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_IMP "' argument");
break;
}
}
rc = ArgsOptionCount(args, OPTION_MOD, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_MOD "' argument");
break;
}
if (pcount) {
prm->modeShowModules = true;
++count;
}
#if 0
rc = ArgsOptionCount(args, OPTION_NEW, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_NEW "' argument");
break;
}
if (pcount) {
prm->modeCreate = true;
++count;
}
#endif
rc = ArgsOptionCount(args, OPTION_DIR, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_DIR "' argument");
break;
}
if (pcount) {
prm->modeShowLoadPath = true;
++count;
}
rc = ArgsOptionCount(args, OPTION_SET, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_SET "' argument");
break;
}
if (pcount) {
rc = ArgsOptionValue(args, OPTION_SET, 0, &prm->setValue);
if (rc == 0) {
const char* p = strchr(prm->setValue, '=');
if (p == NULL || *(p + 1) == '\0') {
rc = RC(rcExe, rcArgv, rcParsing, rcParam, rcInvalid);
LOGERR(klogErr, rc, "Bad " OPTION_SET " value");
break;
}
prm->modeSetNode = true;
prm->modeCreate = prm->modeShowCfg = prm->modeShowEnv
= prm->modeShowFiles = prm->modeShowLoadPath
= prm->modeShowModules = false;
count = 1;
}
}
rc = ArgsOptionCount(args, OPTION_ALL, &pcount);
if (rc) {
LOGERR(klogErr, rc, "Failure to get '" OPTION_ALL "' argument");
break;
}
if (pcount
|| ( !prm->modeShowCfg && ! prm->modeShowLoadPath
&& !prm->modeShowEnv && !prm->modeShowFiles
&& !prm->modeShowModules && !prm->modeCreate
&& !prm->modeSetNode && !prm->ngc))
/* show all by default */
{
prm->modeShowCfg = prm->modeShowEnv = prm->modeShowFiles = true;
#ifndef _STATIC
prm->modeShowModules = true;
#endif
count += 2;
}
if (count > 1)
{ prm->showMultiple = true; }
} while (false);
return rc;
}
rc_t CC KMain ( int argc, char *argv [] )
{
Args * args;
rc_t rc;
rc = ArgsMakeAndHandle (&args, argc, argv, 1, Options, sizeof Options / sizeof (OptDef));
if (rc == 0)
{
uint32_t pcount;
const char * pc;
const char * directory;
const char * archive;
do
{
op_mode mode;
uint32_t ix;
BSTreeInit (&pnames);
rc = ArgsParamCount (args, &pcount);
if (rc)
break;
for (ix = 0; ix < pcount; ++ix)
{
rc = ArgsParamValue (args, ix, (const void **)&pc);
if (rc)
break;
rc = pnamesInsert (pc);
if (rc)
{
PLOGERR (klogInt, (klogInt, rc, "failure to process filter parameter [%s]", pc));
break;
}
}
if (rc)
break;
rc = ArgsOptionCount (args, OPTION_ALIGN, &pcount);
if (rc)
break;
if (pcount == 0)
pc = NULL;
else
{
rc = ArgsOptionValue (args, OPTION_ALIGN, 0, (const void **)&pc);
if (rc)
break;
}
alignment = get_alignment (pc);
if (alignment == sraAlignInvalid)
{
rc = RC (rcExe, rcArgv, rcParsing, rcParam, rcInvalid);
PLOGERR (klogFatal, (klogFatal, rc,
"Parameter for alignment [$(A)] is invalid: must be a power of two bytes",
PLOG_S(A), pc));
break;
}
rc = ArgsOptionCount (args, OPTION_LONGLIST, &pcount);
if (rc)
break;
long_list = (pcount != 0);
rc = ArgsOptionCount (args, OPTION_FORCE, &pcount);
if (rc)
break;
force = (pcount != 0);
mode = OM_NONE;
rc = ArgsOptionCount (args, OPTION_DIRECTORY, &pcount);
if (rc)
break;
if (pcount)
{
rc = ArgsOptionValue (args, OPTION_DIRECTORY, 0, (const void **)&directory);
if (rc)
break;
}
else
directory = NULL;
rc = ArgsOptionCount (args, OPTION_CREATE, &pcount);
if (rc)
break;
if (pcount)
{
rc = ArgsOptionValue (args, OPTION_CREATE, 0, (const void **)&archive);
if (rc)
break;
mode = OM_CREATE;
}
rc = ArgsOptionCount (args, OPTION_TEST, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_TEST;
rc = ArgsOptionValue (args, OPTION_TEST, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
rc = ArgsOptionCount (args, OPTION_LIST, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_TEST;
rc = ArgsOptionValue (args, OPTION_LIST, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
rc = ArgsOptionCount (args, OPTION_EXTRACT, &pcount);
if (rc)
break;
if (pcount)
{
if (mode == OM_NONE)
{
mode = OM_EXTRACT;
rc = ArgsOptionValue (args, OPTION_EXTRACT, 0, (const void **)&archive);
if (rc)
break;
}
else
mode = OM_ERROR;
}
if (mode == OM_NONE)
{
MiniUsage(args);
rc = RC(rcApp, rcArgv, rcParsing, rcParam, rcInsufficient);
break;
}
/* -----
* Mount the native filesystem as root
*/
rc = KDirectoryNativeDir (&kdir);
if (rc != 0)
{
LOGMSG (klogFatal, "Failed to open native KDirectory");
}
else
{
switch (mode)
{
default: /* OM_NONE presumably */
/* assert (mode == OM_NONE); */
/* rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcEmpty); */
/* LOGERR (klogFatal, rc, "Must provide a single operating mode and archive: Create, Test (list) or eXtract"); */
pc = NULL;
break;
case OM_ERROR:
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcAmbiguous);
LOGERR (klogFatal, rc, "Must provide a single operating mode and archive: Create, Test (list) or eXtract");
break;
case OM_CREATE:
STSMSG (2, ("Create Mode %s %s", archive, directory));
if (directory == NULL)
{
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcNull);
LOGERR (klogFatal, rc, "Must provide a directory for create mode");
}
else
rc = run_kar_create (archive, directory);
break;
case OM_TEST:
STSMSG (2, ("Test Mode %s", archive));
rc = run_kar_test (archive);
break;
case OM_EXTRACT:
STSMSG (2, ("Extract Mode %s %s", archive, directory));
if (directory == NULL)
{
rc = RC (rcExe, rcNoTarg, rcParsing, rcParam, rcNull);
LOGERR (klogFatal, rc, "Must provide a directory for extract mode");
}
else
rc = run_kar_extract (archive, directory);
break;
}
KDirectoryRelease (kdir);
}
} while (0);
ArgsWhack (args);
}
if (rc)
LOGERR (klogWarn, rc, "Failure exiting kar");
else
STSMSG (1, ("Success: Exiting kar\n"));
return rc;
}
