static void context_destroy( p_context ctx )
{
if ( ctx == NULL ) return;
free( (char*)ctx->output_file );
free( (char*)ctx->dependency_file );
VNamelistRelease( ctx->include_files );
VNamelistRelease( ctx->src_files );
free( ctx );
}
void release_options( samdump_opts * opts )
{
free_ref_regions( &opts->regions );
if ( opts->qname_prefix != NULL )
free( (void*)opts->qname_prefix );
if ( opts->qual_quant != NULL )
free( (void*)opts->qual_quant );
if( opts->outputfile != NULL )
free( (void*)opts->outputfile );
VNamelistRelease( opts->hdr_comments );
VNamelistRelease( opts->input_files );
VectorWhack ( &opts->mp_dist, release_range_wrapper, NULL );
}
LIB_EXPORT
rc_t CC
XFSOwpListKeys (
const struct XFSOwp * self,
const struct KNamelist ** Keys
)
{
rc_t RCt;
struct VNamelist * List;
RCt = 0;
if ( self == NULL || Keys == NULL ) {
return XFS_RC ( rcNull );
}
* Keys = NULL;
RCt = VNamelistMake ( & List, 16 /* ?? */ );
if ( RCt == 0 ) {
BSTreeForEach (
( BSTree * ) self,
false,
_ListKeysCallback,
List
);
RCt = VNamelistToConstNamelist ( List, Keys );
VNamelistRelease ( List );
}
return RCt;
} /* XFSOwpListKeys () */
rc_t nlt_build_intersect( const KNamelist *nl1, const KNamelist *nl2, const KNamelist ** dst )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
/* loop through nl1: if a entry is found in nl2 -> add it to dst */
uint32_t count;
rc = KNamelistCount( nl1, &count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( nl1, idx, &s );
if ( rc == 0 && s != NULL )
{
if ( nlt_is_name_in_namelist( nl2, s ) )
rc = VNamelistAppend ( v_names, s );
}
}
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, dst );
VNamelistRelease( v_names );
}
return rc;
}
rc_t register_temp_file( temp_registry * self, uint32_t read_id, const char * filename )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcSelf, rcNull );
else if ( filename == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
rc = KLockAcquire ( self -> lock );
if ( rc == 0 )
{
VNamelist * l = VectorGet ( &self -> lists, read_id );
if ( l == NULL )
{
rc = VNamelistMake ( &l, 12 );
if ( rc == 0 )
{
rc = VectorSet ( &self -> lists, read_id, l );
if ( rc != 0 )
VNamelistRelease ( l );
}
}
if ( rc == 0 && l != NULL )
{
rc = VNamelistAppend ( l, filename );
if ( rc == 0 )
rc = Add_File_to_Cleanup_Task ( self -> cleanup_task, filename );
}
KLockUnlock ( self -> lock );
}
}
return rc;
}
rc_t make_column_namelist ( const BSTree *columns, KNamelist **names )
{
VNamelist *list;
rc_t rc = VNamelistMake ( & list, 8 );
if ( rc == 0 )
{
const String *last = NULL;
const VColumnRef *cref = ( const VColumnRef* )
BSTreeFirst ( columns );
while ( cref != NULL )
{
if ( last == NULL || ! StringEqual ( last, & cref -> name ) )
{
rc = VNamelistAppend ( list, cref -> name . addr );
if ( rc != 0 )
break;
last = & cref -> name;
}
cref = ( const VColumnRef* )
BSTNodeNext ( & cref -> n );
}
if ( rc == 0 )
rc = VNamelistToNamelist ( list, names );
VNamelistRelease ( list );
}
return rc;
}
rc_t nlt_copy_namelist( const KNamelist *src, const KNamelist ** dst )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
uint32_t count;
rc = KNamelistCount( src, &count );
if ( rc == 0 )
{
uint32_t idx;
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char *s;
rc = KNamelistGet( src, idx, &s );
if ( rc == 0 && s != NULL )
rc = VNamelistAppend ( v_names, s );
}
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, dst );
VNamelistRelease( v_names );
}
return rc;
}
static void ref_walker_release( struct ref_walker * self )
{
KDirectoryRelease( self->dir );
VDBManagerRelease( self->vmgr );
VSchemaRelease( self->vschema );
AlignMgrRelease ( self->amgr );
VFSManagerRelease ( self->vfs_mgr );
VNamelistRelease ( self->sources );
free_ref_regions( &self->regions );
free( ( void * )self->spot_group );
}
void release_cgi_request( struct cgi_request * request )
{
if ( request != NULL )
{
if ( request->kns_mgr != NULL )
KNSManagerRelease( request->kns_mgr );
if ( request->params != NULL )
VNamelistRelease( request->params );
if ( request->url != NULL )
free( ( void * ) request->url );
free( ( void * ) request );
}
}
static const char * get_db_seq_tbl_name( tool_ctx_t * tool_ctx )
{
const char * res = tool_ctx -> seq_tbl_name;
VNamelist * tables = cmn_get_table_names( tool_ctx -> dir, tool_ctx -> accession_path ); /* cmn_iter.c */
if ( tables != NULL )
{
int32_t idx;
rc_t rc = VNamelistContainsStr( tables, consensus_table, &idx );
if ( rc == 0 && idx > -1 )
res = consensus_table;
VNamelistRelease ( tables );
}
return res;
}
rc_t clear_cgi_request_params( struct cgi_request * request )
{
rc_t rc;
if ( request == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
if ( request->params != NULL )
{
rc = VNamelistRelease( request->params );
if ( rc == 0 )
rc = VNamelistMake( &request->params, 10 );
}
}
return rc;
}
static rc_t clear_tool_options( tool_options * options )
{
rc_t rc = VNamelistRelease ( options->paths );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"VNamelistRelease() failed in $(func)", "func=%s", __func__ ) );
}
if ( options->user_repo_name != NULL )
{
free( (void*) options->user_repo_name );
options->user_repo_name = NULL;
}
return rc;
}
rc_t make_column_typelist ( const BSTree *columns,
const char *col, uint32_t *dflt_idx, KNamelist **typedecls )
{
VNamelist *list;
rc_t rc = VNamelistMake ( & list, 8 );
if ( rc == 0 )
{
uint32_t idx;
const VColumnRef *first;
String col_name;
StringInitCString ( & col_name, col );
first = ( const VColumnRef* )
BSTreeFind ( columns, & col_name, VColumnRefCmpString );
if ( first != NULL )
{
const VColumnRef *cref = ( const VColumnRef* ) BSTNodePrev ( & first -> n );
while ( cref != NULL && StringEqual ( & first -> name, & cref -> name ) )
{
first = cref;
cref = ( const VColumnRef* ) BSTNodePrev ( & cref -> n );
}
for ( cref = first, idx = 0; ; ++ idx )
{
rc = VNamelistAppend ( list, cref -> typedecl );
if ( rc != 0 )
break;
if ( cref -> dflt )
* dflt_idx = idx;
cref = ( const VColumnRef* ) BSTNodeNext ( & cref -> n );
if ( cref == NULL || ! StringEqual ( & first -> name, & cref -> name ) )
break;
}
}
if ( rc == 0 )
rc = VNamelistToNamelist ( list, typedecls );
VNamelistRelease ( list );
}
return rc;
}
rc_t report_clear( p_report self )
{
rc_t rc = 0;
if ( self != NULL )
{
VectorWhack ( &(self->data), report_data_whack, NULL );
VNamelistRelease ( self->columns ); /* ignores NULL */
if ( self->max_width != NULL )
{
free( self->max_width );
self->max_width = NULL;
}
}
else
rc = RC( rcExe, rcNoTarg, rcConstructing, rcSelf, rcNull );
return rc;
}
static rc_t print_headers_by_recalculating( const samdump_opts * opts, input_files * ifs )
{
rc_t rc = KOutMsg( "@HD\tVN:1.3\n" );
if ( rc == 0 )
{
BSTree tree;
/* collect sequenc-id's and names and their lengths, unique by sequence-id */
BSTreeInit( &tree );
rc = build_seq_id_tree( &tree, ifs );
if ( rc == 0 )
{
hdr_print_ctx hctx;
hctx.rc = 0;
hctx.use_seq_id = opts->use_seqid_as_refname;
/* ptrint it */
BSTreeForEach( &tree, false, print_header_callback, &hctx );
rc = hctx.rc;
}
free_seq_id_tree( &tree );
/* collect spot-groups ( unique ) */
if ( rc == 0 )
{
VNamelist * spotgroups;
rc = VNamelistMake( &spotgroups, 10 );
if ( rc == 0 )
{
bool from_stats = false;
rc = extract_spotgroups( spotgroups, ifs, from_stats );
if ( rc == 0 )
rc = print_spotgroups( spotgroups, from_stats );
else
rc = 0; /* otherwise the tool would be not able to handle something that has no headers */
VNamelistRelease( spotgroups );
}
}
}
return rc;
}
rc_t report_set_columns( p_report self, size_t count, ... )
{
rc_t rc;
if ( self != NULL )
{
VNamelistRelease ( self->columns ); /* ignores NULL */
rc = VNamelistMake ( &self->columns, count );
if ( rc == 0 )
{
self->col_count = count;
if ( self->max_width != NULL )
free( self->max_width );
self->max_width = malloc( count * sizeof( *self->max_width ) );
if ( self->max_width == NULL )
rc = RC( rcExe, rcNoTarg, rcConstructing, rcMemory, rcExhausted );
if ( rc == 0 )
{
size_t idx;
va_list args;
va_start ( args, count );
for ( idx = 0; idx < count && rc == 0; ++idx )
{
const char * s = va_arg( args, const char * );
if ( s != NULL )
{
rc = VNamelistAppend ( self->columns, s );
self->max_width[ idx ] = string_size( s );
}
else
{
rc = VNamelistAppend ( self->columns, "." );
self->max_width[ idx ] = 1;
}
}
va_end ( args );
}
LIB_EXPORT rc_t CC KDlsetList ( const KDlset *self, KNamelist **listp )
{
list_dylib_param pb;
assert ( listp != NULL );
if ( self == NULL )
pb . rc = RC ( rcFS, rcDylib, rcListing, rcSelf, rcNull );
else
{
pb . rc = VNamelistMake ( & pb . list, VectorLength ( & self -> name ) );
if ( pb . rc == 0 )
{
bool fail = VectorDoUntil ( & self -> name, false, list_dylib, & pb );
if ( ! fail )
pb . rc = VNamelistToNamelist ( pb . list, listp );
VNamelistRelease ( pb . list );
}
}
return pb . rc;
}
rc_t nlt_make_namelist_from_string( const KNamelist **list, const char * src )
{
VNamelist *v_names;
rc_t rc = VNamelistMake ( &v_names, 5 );
if ( rc == 0 )
{
char * s = string_dup_measure ( src, NULL );
if ( s )
{
uint32_t str_begin = 0;
uint32_t str_end = 0;
char c;
do
{
c = s[ str_end ];
if ( c == ',' || c == 0 )
{
if ( str_begin < str_end )
{
char c_temp = c;
s[ str_end ] = 0;
rc = VNamelistAppend ( v_names, &(s[str_begin]) );
s[ str_end ] = c_temp;
}
str_begin = str_end + 1;
}
str_end++;
} while ( c != 0 && rc == 0 );
free( s );
}
if ( rc == 0 )
rc = VNamelistToConstNamelist ( v_names, list );
VNamelistRelease( v_names );
}
return rc;
}
static rc_t print_headers_from_file( const samdump_opts * opts )
{
KDirectory * dir;
rc_t rc = KDirectoryNativeDir ( &dir );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant created native directory for file '$(t)'", "t=%s", opts->header_file ) );
}
else
{
const struct KFile * f;
rc = KDirectoryOpenFileRead ( dir, &f, "%s", opts->header_file );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant open file '$(t)'", "t=%s", opts->header_file ) );
}
else
{
VNamelist * headers;
rc = VNamelistMake ( &headers, 25 );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant create container for file '$(t)'", "t=%s", opts->header_file ) );
}
else
{
rc = LoadKFileToNameList( f, headers );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant load file '$(t)' into container", "t=%s", opts->header_file ) );
}
else
{
uint32_t count;
rc = VNameListCount ( headers, &count );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant get count for container of '$(t)'", "t=%s", opts->header_file ) );
}
else
{
uint32_t i;
for ( i = 0; i < count && rc == 0; ++i )
{
const char * line;
rc = VNameListGet ( headers, i, &line );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cant get line #$(t) from container", "t=%u", i ) );
}
else
{
rc = KOutMsg( "%s\n", line );
}
}
}
}
VNamelistRelease ( headers );
}
KFileRelease ( f );
}
KDirectoryRelease ( dir );
}
return rc;
}
static void CC destroy_list( void * item, void * data )
{
if ( item != NULL )
VNamelistRelease ( item );
}
static rc_t gather_string_options( Args * args, samdump_opts * opts )
{
const char * s;
uint32_t count;
rc_t rc = get_str_option( args, OPT_PREFIX, &s );
if ( rc == 0 && s != NULL )
{
opts->qname_prefix = string_dup_measure( s, NULL );
if ( opts->qname_prefix == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing QNAME-PREFIX" );
}
}
if ( rc == 0 )
{
rc = get_str_option( args, OPT_Q_QUANT, &s );
if ( rc == 0 && s != NULL )
{
opts->qual_quant = string_dup_measure( s, NULL );
if ( opts->qual_quant == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing QUAL-QUANT" );
}
else
{
bool bres = QualityQuantizerInitMatrix( opts->qual_quant_matrix, opts->qual_quant );
if ( !bres )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcParam, rcInvalid );
(void)LOGERR( klogErr, rc, "error initializing quality-quantizer-matrix" );
}
}
}
}
if ( rc == 0 )
{
rc = get_str_option( args, OPT_OUTPUTFILE, &s );
if ( rc == 0 && s != NULL )
{
opts->outputfile = string_dup_measure( s, NULL );
if ( opts->outputfile == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing OUTPUTFILE" );
}
}
}
if ( rc == 0 )
{
rc = ArgsOptionCount( args, OPT_HDR_COMMENT, &count );
if ( rc == 0 && count > 0 )
{
uint32_t i;
rc = VNamelistMake( &opts->hdr_comments, 10 );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * src;
rc = ArgsOptionValue( args, OPT_HDR_COMMENT, i, &src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline option '$(t)' #$(n)",
"t=%s,n=%u", OPT_HDR_COMMENT, i ) );
}
else
{
rc = VNamelistAppend( opts->hdr_comments, src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error appending hdr-comment '$(t)'",
"t=%s", src ) );
}
}
}
if ( rc != 0 )
{
VNamelistRelease( opts->hdr_comments );
opts->hdr_comments = NULL;
}
}
}
if ( rc == 0 )
{
rc = ArgsParamCount( args, &count );
if ( rc == 0 && count > 0 )
{
uint32_t i;
rc = VNamelistMake( &opts->input_files, 10 );
for ( i = 0; i < count && rc == 0; ++i )
{
const char * src;
rc = ArgsParamValue( args, i, &src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error retrieving comandline param #$(n)",
"n=%u", i ) );
}
else
{
rc = VNamelistAppend( opts->input_files, src );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "error appending input_file '$(t)'",
"t=%s", src ) );
}
}
}
if ( rc != 0 )
{
VNamelistRelease( opts->input_files );
opts->input_files = NULL;
}
}
opts->input_file_count = count;
}
rc = get_str_option( args, OPT_CIGAR_TEST, &s );
if ( rc == 0 && s != NULL )
{
opts->cigar_test = string_dup_measure( s, NULL );
if ( opts->cigar_test == NULL )
{
rc = RC( rcExe, rcNoTarg, rcValidating, rcMemory, rcExhausted );
(void)LOGERR( klogErr, rc, "error storing CIGAR-TEST" );
}
}
return rc;
}
static void CC report_data_whack( void *item, void *data )
{
const VNamelist * values = item;
if ( values != NULL )
VNamelistRelease ( values );
}
/* ListPhysColumns
* avail: 2.4
*/
LIB_EXPORT rc_t CC VTableListPhysColumns ( const VTable *self, KNamelist **names )
{
rc_t rc;
if ( names == NULL )
rc = RC ( rcVDB, rcTable, rcListing, rcParam, rcNull );
else
{
* names = NULL;
if ( self == NULL )
rc = RC ( rcVDB, rcTable, rcListing, rcSelf, rcNull );
else
{
KNamelist *kcol_names;
rc = KTableListCol ( self -> ktbl, & kcol_names );
if ( rc == 0 )
{
uint32_t kcol_count;
rc = KNamelistCount ( kcol_names, & kcol_count );
if ( rc == 0 )
{
uint32_t scol_count = 0;
KNamelist *scol_names = NULL;
const KMDataNode *col_node = self -> col_node;
#if LAZY_OPEN_COL_NODE
if ( col_node == NULL )
{
rc = KMetadataOpenNodeRead ( self -> meta, & ( ( VTable* ) self ) -> col_node, "col" );
if ( rc == 0 || GetRCState ( rc ) != rcNotFound )
col_node = self -> col_node;
}
#endif
if ( col_node != NULL )
{
rc = KMDataNodeListChildren ( col_node, & scol_names );
if ( rc == 0 )
rc = KNamelistCount ( scol_names, & scol_count );
}
if ( rc == 0 )
{
VNamelist *vnames;
rc = VNamelistMake ( & vnames, kcol_count + scol_count );
if ( rc == 0 )
{
uint32_t i;
const char *name;
for ( i = 0; i < kcol_count && rc == 0; ++ i )
{
rc = KNamelistGet ( kcol_names, i, & name );
if ( rc == 0 )
rc = VNamelistAppend ( vnames, name );
}
for ( i = 0; i < scol_count && rc == 0; ++ i )
{
rc = KNamelistGet ( scol_names, i, & name );
if ( rc == 0 )
rc = VNamelistAppend ( vnames, name );
}
if ( rc == 0 )
{
rc = VNamelistToNamelist ( vnames, names );
if ( rc == 0 )
VNamelistReorder ( vnames, false );
}
}
VNamelistRelease ( vnames );
}
KNamelistRelease ( scol_names );
}
KNamelistRelease ( kcol_names );
}
}
}
return rc;
}
LIB_EXPORT
rc_t CC
XFS_SimpleTokenize_ZHR (
const char * SimpleString,
char Separator,
struct KNamelist ** Tokens
)
{
rc_t RCt;
struct VNamelist * List;
char LN [ XFS_SIZE_1024 ], * LNEnd;
const char * End;
RCt = 0;
List = NULL;
LNEnd = NULL;
End = NULL;
if ( Tokens == NULL || SimpleString == NULL ) {
return XFS_RC ( rcNull );
}
* Tokens = NULL;
RCt = VNamelistMake ( & List, 16 /* he-he */ );
if ( RCt == 0 ) {
End = SimpleString;
LNEnd = LN;
while ( * End != 0 ) {
* LNEnd = * End;
if ( * End == Separator ) {
*LNEnd = 0;
RCt = _AddTrimStringToList_ZHR ( List, LN );
if ( RCt != 0 ) {
break;
}
LNEnd = LN;
End ++;
}
else {
End ++;
LNEnd ++;
}
}
if ( RCt == 0 ) {
if ( LN != LNEnd ) {
* LNEnd = 0;
RCt = _AddTrimStringToList_ZHR ( List, LN );
}
}
if ( RCt == 0 ) {
RCt = VNamelistToNamelist ( List, Tokens );
}
VNamelistRelease ( List );
}
return RCt;
} /* XFS_SimpleTokenize_ZHR () */
