Problem with empty results

[dputhier]

This is the follow up of our discussion about a "pointer being freed was not allocated".

Looking at the code I realized that the problem is simply related to the fact that the expected result is and empty gtf_data.

I have tried to explain clearly the sequence of actions below.

  In [1]: from gtftk.utils import get_example_file
     ...: from gtftk.gtf_interface import GTF
     ...: a_file = get_example_file("simple", "gtf")[1]
     ...: # Let's create a GTF
     ...: gtf = GTF(a_file)
     ...: # The pointer to the GTF_DATA is
     ...: gtf._data
     ...: 
     ...: # Now we ask for a new pointer and this is what we get.
     ...: # The pointer points to 2 transcripts ['G0007T001', 'G0007T002']
     ...: ptr_1 = gtf._dll.select_by_key(gtf._data, 'transcript_id', ",".join(['G0007T001', 'G0007T002']), 0)
     ...: ptr_1
     ...: 
  Out[1]: <cdata 'GTF_DATA *' 0x7fb90724b150>

  In [2]: ptr_1.size 
  Out[2]: 6

  In [3]: # We pass this pointer to the the _clone method just 
     ...: # to embed this pointer in a GTF object.
     ...: # This pointer has the same address as the previous one
     ...: # since the gtf2 object (an instance of GTF class) is just a container
     ...: gtf_2 = gtf._clone(ptr_1)
     ...: gtf_2._data
     ...: 
  Out[3]: <cdata 'GTF_DATA *' 0x7fb90724b150>

  In [4]: # The GTF instance is funtional and we can call it with several methods
     ...: # For instance we can see that it contains the 2 expected transcripts
     ...: gtf_2.get_tx_ids(nr=True)
  Out[4]: ['G0007T001', 'G0007T002']

  In [5]: 

  In [5]: # We could select exons also
     ...: gtf_2.select_by_key("feature", "exon").extract_data("exon_id", as_list=True)
     ...: 
  Out[5]: ['G0007T002E001', 'G0007T001E001']

  In [6]: # Now we pass this pointer to another function of the
     ...: # dynamic library. if we pass it to a function that is expected to return something,
     ...: # everything is OK. 
     ...: # Here we will delete the exons
     ...: ptr_2 = gtf_2._dll.select_by_key(gtf_2._data, "feature", "exon", 1)
     ...: ptr_2.size
     ...: 
  Out[6]: 4

  In [7]: # Now if we ask for something that is non existing
     ...: ptr_2 = gtf_2._dll.select_by_key(gtf_2._data, "feature", "gene", 0)
  python(52707,0x7fff70ef4000) malloc: *** error for object 0x10df80002: pointer being freed was not allocated
  *** set a breakpoint in malloc_error_break to debug
  Abort trap: 6

I think this shows that this is not related to any issue in _clone or whatever on the C side. This is just the fact that we don't know maybe how to deal with an empty result. Tell me