[ensembl-dev] bugs in blastz-chain-net pipeline

[Sharon Wei]

Hi Ensembl Compara team,

I recently updated our local blastz pipeline to ensembl-65 code, and 
have found two places where there seem to be a bug.

1. In 
ensembl-analysis/modules/Bio/EnsEMBL/Analysis/Runnable/AlignmentNets.pm
line 394:      $fp->level_id($level_id);
The $fp is a GenomicAlignBlock object, and this object has no function 
level_id(), only GenomicAlign has this function.
So I changed it to
    map {$_->level_id($level_id)} @{$fp->genomic_align_array()};


2. In ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
In function CreateNewJob(), the following doesn't make sense and I had 
to comment it out to make the pipeline work.
throw("Please specify prev_job object instead of input_job_id if 
available") if ($prev_job_id);

sub CreateNewJob {
   my ($class, @args) = @_;

   return undef unless(scalar @args);

   my ($input_id, $analysis, $prev_job, $prev_job_id, $blocked, 
$semaphore_count, $semaphored_job_id) =
      rearrange([qw(INPUT_ID ANALYSIS PREV_JOB INPUT_JOB_ID BLOCK 
SEMAPHORE_COUNT SEMAPHORED_JOB_ID)], @args);

   throw("must define input_id") unless($input_id);
   throw("must define analysis") unless($analysis);
   throw("analysis must be [Bio::EnsEMBL::Analysis] not a [$analysis]")
     unless($analysis->isa('Bio::EnsEMBL::Analysis'));
   throw("analysis must have adaptor connected to database")
     unless($analysis->adaptor and $analysis->adaptor->db);
   throw("Please specify prev_job object instead of input_job_id if 
available") if ($prev_job_id);   # 'obsolete' message

   $prev_job_id = $prev_job && $prev_job->dbID();

         # if the user did not specifically ask for a new fan, consider 
propagation:


Sharon