static rc_t vdb_info_print_xml_uint64( const char * tag, const uint64_t value )
{
if ( value != 0 )
return KOutMsg( "<%s>%lu<%s>\n", tag, value, tag );
else
return 0;
}
rc_t CC Usage (const Args * args)
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
rc_t rc;
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
UsageSummary (progname);
KOutMsg ("\n"
"Option:\n");
HelpOptionLine (ALIAS_FORCE, OPTION_FORCE, NULL, force_usage);
HelpOptionLine (ALIAS_PRESERVE, OPTION_PRESERVE, NULL, preserve_usage);
HelpOptionLine (ALIAS_RECURSE, OPTION_RECURSE, NULL, recurse_usage);
HelpOptionLine (ALIAS_TEST, OPTION_TEST, NULL, test_usage);
HelpOptionsStandard ();
HelpVersion (fullpath, KAppVersion());
return rc;
}
static rc_t vdb_info_print_json_s( const char * tag, const char * value )
{
if ( value[ 0 ] != 0 )
return KOutMsg( "\"%s\":\"%s\",\n", tag, value );
else
return 0;
}
static rc_t copy_metadata_attribs ( const KMDataNode *snode, KMDataNode *dnode,
const char *node_path, const bool show_meta )
{
KNamelist *attrs;
uint32_t i, count;
rc_t rc = KMDataNodeListAttr ( snode, & attrs );
DISP_RC( rc, "copy_metadata_child:KMDataNodeListAttr(src) failed" );
if ( rc != 0 ) return rc;
rc = KNamelistCount ( attrs, & count );
for ( i = 0; rc == 0 && i < count; ++ i )
{
const char *attr;
rc = KNamelistGet ( attrs, i, & attr );
if ( rc == 0 )
{
char buffer [ 1024 ];
size_t bytes;
/* test for attr existence */
rc = KMDataNodeReadAttr ( dnode, attr, buffer, sizeof buffer, & bytes );
if ( rc != 0 )
{
rc = KMDataNodeReadAttr ( snode, attr, buffer, sizeof buffer, & bytes );
if ( rc == 0 )
{
if ( show_meta )
KOutMsg( "copy atr %s : %s\n", node_path, attr );
rc = KMDataNodeWriteAttr ( dnode, attr, buffer );
}
}
}
DISP_RC( rc, "copy_metadata_child:failed to copy attribute" );
}
KNamelistRelease ( attrs );
return rc;
}
static rc_t vdb_info_print_xml_s( const char * tag, const char * value )
{
if ( value[ 0 ] != 0 )
return KOutMsg( "<%s>%s</%s>\n", tag, value, tag );
else
return 0;
}
static rc_t CC pileup_v2_exit_ref_pos( ref_walker_data * rwd )
{
pileup_v2_ctx * ctx = rwd->data;
rc_t rc = KOutMsg( "%s\t%u\t%c\t%u\t", rwd->ref_name, rwd->pos + 1, rwd->ascii_ref_base, rwd->depth );
if ( rc == 0 )
rc = print_dyn_string( ctx->bases );
if ( rc == 0 && ctx->print_qual )
{
rc = KOutMsg( "\t" );
if ( rc == 0 )
rc = print_dyn_string( ctx->qual );
}
if ( rc == 0 )
rc = KOutMsg( "\n" );
return rc;
}
static rc_t enter_vdbcopy_node( KMetadata *dst_meta, const bool show_meta )
{
rc_t rc;
KMDataNode *hist_node;
if ( show_meta )
KOutMsg( "--- entering Copy entry...\n" );
rc = KMetadataOpenNodeUpdate ( dst_meta, &hist_node, "HISTORY" );
DISP_RC( rc, "enter_vdbcopy_node:KMetadataOpenNodeUpdate('HISTORY') failed" );
if ( rc == 0 )
{
char event_name[ 32 ];
uint32_t index = get_child_count( hist_node ) + 1;
rc = string_printf ( event_name, sizeof( event_name ), NULL, "EVENT_%u", index );
DISP_RC( rc, "enter_vdbcopy_node:string_printf(EVENT_NR) failed" );
if ( rc == 0 )
{
KMDataNode *event_node;
rc = KMDataNodeOpenNodeUpdate ( hist_node, &event_node, event_name );
DISP_RC( rc, "enter_vdbcopy_node:KMDataNodeOpenNodeUpdate('EVENT_NR') failed" );
if ( rc == 0 )
{
rc = enter_date_name_vers( event_node );
KMDataNodeRelease ( event_node );
}
}
KMDataNodeRelease ( hist_node );
}
return rc;
}
rc_t CC Usage (const Args * args)
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
rc_t rc;
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
if (rc)
progname = fullpath = UsageDefaultName;
UsageSummary (progname);
KOutMsg ("Options:\n");
HelpOptionLine (ALIAS_LITE, OPTION_LITE, NULL, lite_usage);
#if USE_FORCE
HelpOptionLine (ALIAS_FORCE, OPTION_FORCE, NULL, force_usage);
#endif
HelpOptionsStandard ();
HelpVersion (fullpath, KAppVersion());
return rc;
}
rc_t CC UsageSummary ( const char * progname )
{
return KOutMsg ( "\n"
"Usage:\n"
" %s <sra-accession> <gtf-file> [options]\n"
"\n", progname );
}
/* -------------------------------------------------------------------- */
rc_t temp_registry_merge( temp_registry * self,
KDirectory * dir,
const char * output_filename,
size_t buf_size,
bool show_progress,
bool force,
compress_t compress )
{
rc_t rc = 0;
if ( self == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcSelf, rcNull );
else if ( output_filename == NULL )
rc = RC( rcVDB, rcNoTarg, rcConstructing, rcParam, rcNull );
else
{
struct bg_progress * progress = NULL;
if ( show_progress )
{
rc = KOutMsg( "concat :" );
if ( rc == 0 )
{
uint64_t total = total_size( dir, &self -> lists );
rc = bg_progress_make( &progress, total, 0, 0 ); /* progress_thread.c */
}
}
if ( rc == 0 )
{
uint32_t first;
uint32_t count = count_valid_entries( &self -> lists, &first ); /* above */
if ( count == 1 )
{
/* we have only ONE set of files... */
VNamelist * l = VectorGet ( &self -> lists, first );
VNamelistReorder ( l, false );
rc = execute_concat( dir,
output_filename,
l,
buf_size,
progress,
force,
compress ); /* concatenator.c */
}
else if ( count > 1 )
{
/* we have MULTIPLE sets of files... */
cmn_merge cmn = { dir, output_filename, buf_size, progress, force, compress };
on_merge_ctx omc = { &cmn, 0 };
VectorInit( &omc . threads, 0, count );
VectorForEach ( &self -> lists, false, on_merge, &omc );
join_and_release_threads( &omc . threads ); /* helper.c */
}
bg_progress_release( progress ); /* progress_thread.c ( ignores NULL )*/
}
}
return rc;
}
rc_t CC UsageSummary ( const char * progname )
{
return KOutMsg ("\n"
"Usage:\n"
" %s src-path dst-path [options]\n"
"\n", progname);
return 0;
}
static rc_t CC on_history_path( const String * part, void *data )
{
tool_options * options = data;
rc_t rc = add_tool_options_path( options, part->addr );
if ( options -> detailed )
KOutMsg( "source: %S\n", part );
return rc;
}
rc_t CC UsageSummary ( const char * progname )
{
return KOutMsg (
"\n"
"Usage:\n"
" %s [options] -f <url | accession> -d <dst_path> -c no\n"
"\n", progname );
}
rc_t CC Usage ( const Args * args )
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
rc_t rc;
if ( args == NULL )
rc = RC ( rcApp, rcArgv, rcAccessing, rcSelf, rcNull );
else
{
rc = ArgsProgram ( args, &fullpath, &progname );
if ( rc != 0 )
progname = fullpath = UsageDefaultName;
rc = UsageSummary ( progname );
if ( rc != 0 )
{
PLOGERR( klogErr, ( klogErr, rc,
"UsageSummary() failed in $(func)", "func=%s", __func__ ) );
}
else
rc = KOutMsg ( "Options:\n" );
if ( rc == 0 )
{
uint32_t idx, count = sizeof ToolOptions / sizeof ToolOptions [ 0 ];
for ( idx = 0; idx < count; ++idx )
{
OptDef * o = &ToolOptions[ idx ];
HelpOptionLine ( o->aliases, o->name, NULL, o->help );
}
}
if ( rc == 0 )
rc = KOutMsg ( "\n" );
if ( rc == 0 )
{
HelpOptionsStandard ();
HelpVersion ( fullpath, KAppVersion() );
}
}
return rc;
}
rc_t CC UsageSummary ( const char * progname )
{
return KOutMsg (
"\n"
"Usage:\n"
" %s\n"
"\n", progname );
}
static void CC print_header_callback( BSTNode *n, void *data )
{
seq_id_node * node = ( seq_id_node * )n;
hdr_print_ctx * hctx = ( hdr_print_ctx * )data;
if ( hctx->rc == 0 )
{
if ( hctx->use_seq_id )
hctx->rc = KOutMsg( "@SQ\tSN:%s\tLN:%u\n", node->seq_id, node->seq_len );
else
{
if ( cmp_pchar_0( node->seq_id, node->name ) == 0 )
hctx->rc = KOutMsg( "@SQ\tSN:%s\tLN:%u\n", node->name, node->seq_len );
else
hctx->rc = KOutMsg( "@SQ\tSN:%s\tAS:%s\tLN:%u\n", node->name, node->seq_id, node->seq_len );
}
}
}
static rc_t report_ref_loc( const VDBManager *vdb_mgr, VFSManager * vfs_mgr, const char * seq_id )
{
const String * path;
rc_t rc = resolve_accession( vfs_mgr, seq_id, &path );
if ( rc == 0 )
{
rc = KOutMsg( "location:\t%S\n", path );
if ( rc == 0 )
{
uint32_t pt = VDBManagerPathType ( vdb_mgr, "%S", path );
const char * spt = path_type_2_str( pt );
rc = KOutMsg( "pathtype:\t%s\n", spt );
}
free ( (void*) path );
}
return rc;
}
rc_t CC UsageSummary(const char *progname) {
KOutMsg("Update user's NCBI VDB crypto password\n"
"If not run with --quiet recommendations\n"
"are given if errors are detected.\n"
"\n");
return 0;
}
static rc_t perform_unlock( visit_ctx * octx )
{
rc_t rc = 0;
unlock_data data;
memset( &data, 0, sizeof data );
octx->data = &data;
if ( rc == 0 )
rc = foreach_path( octx, on_unlock_path );
if ( rc == 0 )
rc = KOutMsg( "-----------------------------------\n" );
if ( rc == 0 )
rc = KOutMsg( "%,u lock-files removed\n", data.lock_count );
return rc;
}
static rc_t vdb_fastq_loop_with_name( const p_dump_context ctx, const fastq_ctx * fctx )
{
rc_t rc = 0;
int64_t row_id;
vdn_start( ctx->row_generator );
while ( vdn_next( ctx->row_generator, (uint64_t*)&row_id ) && rc == 0 )
{
rc = Quitting();
if ( rc == 0 )
{
uint32_t elem_bits, boff, row_len, name_len;
const char * data;
const char * name;
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_name, &elem_bits,
(const void**)&name, &boff, &name_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), NAME ) failed", rc, row_id );
else
{
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_read, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), READ ) failed", rc, row_id );
else
{
rc = KOutMsg( "@%s.%li %.*s length=%u\n%.*s\n",
fctx->run_name, row_id, name_len, name, row_len, row_len, data );
if ( rc == 0 )
{
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_qual, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), QUALITY ) failed", rc, row_id );
else
rc = KOutMsg( "+%s.%li %.*s length=%u\n%.*s\n",
fctx->run_name, row_id, name_len, name, row_len, row_len, data );
}
}
}
}
}
return rc;
}
static rc_t perform_report( visit_ctx * octx )
{
rc_t rc = 0;
report_data data;
memset( &data, 0, sizeof data );
octx->data = &data;
if ( octx->options->detailed )
rc = KOutMsg( "\n-----------------------------------\n" );
if ( rc == 0 )
rc = foreach_path( octx, on_report_path );
if ( rc == 0 )
rc = KOutMsg( "-----------------------------------\n" );
if ( rc == 0 )
rc = KOutMsg( "%,u cached file(s)\n", data.partial_count );
if ( rc == 0 )
rc = KOutMsg( "%,u complete file(s)\n", data.full_count );
if ( rc == 0 )
rc = KOutMsg( "%,u bytes in cached files\n", data.file_size );
if ( rc == 0 )
rc = KOutMsg( "%,u bytes used in cached files\n", data.used_file_size );
if ( rc == 0 )
rc = KOutMsg( "%,u lock files\n", data.lock_count );
return rc;
}
rc_t CC UsageSummary (const char * progname) {
return KOutMsg (
"Usage:\n"
" %s [options] [<query> ...]\n"
"\n"
"Summary:\n"
" Display VDB configuration information\n"
"\n", progname);
}
rc_t CC UsageSummary ( const char *prog_name )
{
return KOutMsg ( "Usage: %s [options] src-object dst-object\n"
" %s [options] src-object [src-object...] dst-dir\n"
"\n"
, prog_name
, prog_name
);
}
void debug_cigar_t( const struct cigar_t * c )
{
if ( c != NULL )
{
int i;
for ( i = 0; i < c->length; ++i )
KOutMsg( "c[%d]: %d x %c\n", i, c->count[ i ], c->op[ i ] );
}
}
rc_t CC UsageSummary (const char * progname) {
return KOutMsg (
"Usage:\n"
" %s [options] <db-path>\n"
"\n"
"Summary:\n"
" Print database alignment information\n"
"\n", progname);
}
static void CC skiplist_report_cb( BSTNode *n, void *data )
{
const struct skiplist_ref_node * node = ( const struct skiplist_ref_node * )n;
uint32_t nr = VectorLength( &( node->skip_ranges ) );
KOutMsg( "\n-[%s]:\n", node->name );
if ( n == 0 )
KOutMsg( " no ranges!\n" );
else
{
uint32_t i;
for ( i = 0; i < nr; ++i )
{
const struct skip_range * sr = ( const struct skip_range * ) VectorGet ( &( node->skip_ranges ), i );
KOutMsg( " %u ... %u\n", sr->start, sr->end );
}
}
}
static rc_t print_headers_from_metadata( const VDatabase * db, bool * recalc, const char * path )
{
const KMetadata * meta;
rc_t rc = VDatabaseOpenMetadataRead( db, &meta );
if ( rc != 0 )
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot open metadata from '$(t)'", "t=%s", path ) );
else
{
const KMDataNode * node;
rc = KMetadataOpenNodeRead( meta, &node, "BAM_HEADER" );
if ( rc != 0 )
{
if ( GetRCState( rc ) == rcNotFound )
{
*recalc = true;
rc = 0;
}
else
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot open meta-node 'BAM_HEADER' from '$(t)'", "t=%s", path ) );
}
else
{
size_t offset = 0, num_read, remaining = ~0;
char buffer[ 40960 ];
while ( rc == 0 && remaining > 0 )
{
rc = KMDataNodeRead( node, offset, buffer, sizeof( buffer ),
&num_read, &remaining );
if ( rc == 0 )
{
rc = KOutMsg( "%.*s", ( uint32_t )num_read, buffer );
offset += num_read;
}
}
if ( rc == 0 && buffer[ num_read - 1 ] != '\n' )
{
rc = KOutMsg( "\n" );
}
KMDataNodeRelease( node );
}
KMetadataRelease( meta );
}
return rc;
}
rc_t dump_quality_33( samdump_opts * opts, char const *quality, uint32_t qual_len, bool reverse )
{
rc_t rc = 0;
bool quantize = ( opts->qual_quant != NULL );
uint32_t i;
if ( reverse )
{
if ( quantize )
{
for ( i = 0; i < qual_len && rc == 0; ++i )
{
uint32_t qual = quality[ qual_len - i - 1 ] - 33;
char newValue = ( opts->qual_quant_matrix[ qual ] + 33 );
rc = KOutMsg( "%c", newValue );
}
}
else
{
for ( i = 0; i < qual_len && rc == 0; ++i )
{
char qual = quality[ qual_len - i - 1 ];
rc = KOutMsg( "%c", qual );
}
}
}
else
{
if ( quantize )
{
for ( i = 0; i < qual_len && rc == 0; ++i )
{
uint32_t qual = quality[ i ] - 33;
char newValue = opts->qual_quant_matrix[ qual ] + 33;
rc = KOutMsg( "%c", newValue );
}
}
else
{
rc = KOutMsg( "%.*s", qual_len, quality );
}
}
return rc;
}
static rc_t vdi_report_repo_str( const KRepository * repo, const char * elem_name, repofunc f )
{
if ( f != NULL )
{
char buffer[ 4096 ];
rc_t rc = f( repo, buffer, sizeof buffer, NULL );
if ( rc == 0 ) return KOutMsg( " - %s : %s\n", elem_name, buffer );
}
return 0;
}
static rc_t vdb_fasta_loop_without_name( const p_dump_context ctx, const fastq_ctx * fctx )
{
rc_t rc = 0;
int64_t row_id;
vdn_start( ctx->row_generator );
while ( vdn_next( ctx->row_generator, (uint64_t*)&row_id ) && rc == 0 )
{
rc = Quitting();
if ( rc == 0 )
{
uint32_t elem_bits, boff, row_len;
const char * data;
rc = VCursorCellDataDirect( fctx->cursor, row_id, fctx->idx_read, &elem_bits,
(const void**)&data, &boff, &row_len );
if ( rc != 0 )
vdb_fastq_row_error( "VCursorCellDataDirect( row#$(row_nr), READ ) failed", rc, row_id );
else
{
uint32_t idx = 0;
int32_t to_print = row_len;
rc = KOutMsg( ">%s.%li %li length=%u\n",
fctx->run_name, row_id, row_id, row_len );
if ( to_print > ctx->max_line_len )
to_print = ctx->max_line_len;
while ( rc == 0 && to_print > 0 )
{
rc = KOutMsg( "%.*s\n", to_print, &data[ idx ] );
if ( rc == 0 )
{
idx += ctx->max_line_len;
to_print = ( row_len - idx );
if ( to_print > ctx->max_line_len )
to_print = ctx->max_line_len;
}
}
}
}
}
return rc;
}
