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; ...@@ -131,7 +131,7 @@ $delete = $force_delete if $force_delete;
delete_existing_xrefs($xref_db) if ($delete); delete_existing_xrefs($xref_db) if ($delete);
check_existing_and_exit($oligo_db, $xref_db);#??? check_existing_and_exit($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){ if ($health_check){
print "Healthcheck passed\n"; print "Healthcheck passed\n";
exit 0; exit 0;
...@@ -351,14 +351,9 @@ foreach my $key (keys %transcript_probeset_count) { ...@@ -351,14 +351,9 @@ foreach my $key (keys %transcript_probeset_count) {
#This is inc'ing an undef? #This is inc'ing an undef?
$transcripts_per_probeset{$probeset}++; $transcripts_per_probeset{$probeset}++;
# only create xrefs for non-promiscuous probesets
#XXX
#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} <= $max_transcripts_per_probeset) { if ($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$hits\n"; print LOG "$probeset\t$transcript\tmapped\t$probeset_size\t$hits\n";
} }
...@@ -375,7 +370,8 @@ foreach my $key (keys %transcript_probeset_count) { ...@@ -375,7 +370,8 @@ foreach my $key (keys %transcript_probeset_count) {
if (!$no_triage) { if (!$no_triage) {
#Can/should we concentrate all unmapped info into one record #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', $um_obj = new Bio::EnsEMBL::UnmappedObject(-type => 'probe2transcript',
-analysis => $analysis, -analysis => $analysis,
...@@ -910,7 +906,7 @@ sub usage { ...@@ -910,7 +906,7 @@ sub usage {
[--no_triage] Don't write to the unmapped_object/unmapped_reason tables. [--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. [--help] This text.
......
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