Commit 1993748a authored by Nathan Johnson's avatar Nathan Johnson
Browse files

a bit more docs and fixed array name in add_xref call

parent c0930f9c
......@@ -131,7 +131,7 @@ $delete = $force_delete if $force_delete;
delete_existing_xrefs($xref_db) if ($delete);
check_existing_and_exit($oligo_db, $xref_db);#???
#Do we need this healthcheck mode now? We're doing it all anyway and fails if any tests fail
if ($health_check){
print "Healthcheck passed\n";
exit 0;
......@@ -351,14 +351,9 @@ foreach my $key (keys %transcript_probeset_count) {
#This is inc'ing an undef?
# only create xrefs for non-promiscuous probesets
#add_xref($transcript_ids{$transcript}, $probeset, $db_entry_adaptor, $array_name_cache{$array}, $probeset_size, $hits);
#print LOG "$probeset\t$transcript\tmapped\t$probeset_size\t$hits\n";
if ($transcripts_per_probeset{$probeset} <= $max_transcripts_per_probeset) {
add_xref($transcript_ids{$transcript}, $probeset, $db_entry_adaptor, $array, $probeset_size, $hits);
add_xref($transcript_ids{$transcript}, $probeset, $db_entry_adaptor, $array_name_cache{$array}, $probeset_size, $hits);
print LOG "$probeset\t$transcript\tmapped\t$probeset_size\t$hits\n";
......@@ -375,7 +370,8 @@ foreach my $key (keys %transcript_probeset_count) {
if (!$no_triage) {
#Can/should we concentrate all unmapped info into one record
#Currently getting one for each probe and each probeset
#Currently getting one for each probe and each probeset?
#Or is this a problem with array association i.e. Collapse not warked properly?
$um_obj = new Bio::EnsEMBL::UnmappedObject(-type => 'probe2transcript',
-analysis => $analysis,
......@@ -910,7 +906,7 @@ sub usage {
[--no_triage] Don't write to the unmapped_object/unmapped_reason tables.
[--health_check] Only do sanity checks, then stop.
[--health_check] Only do sanity checks, then stop. Useful for capthing errors before nohuping the process proper.
[--help] This text.
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