--phased option throwing error

[tzhughes]

$h/bin/arch/genmod-0.9.7/scripts/run_genmod.py -phased -v -at gtf standardTrio.fam truePositives.vcf ../Homo_sapiens.GRCh37.75_partChr1andX.gtf is working fine, but when running with the --phased option, I get:

$h/bin/arch/genmod-0.9.7/scripts/run_genmod.py -phased -v -at gtf standardTrio.fam truePositives.vcf ../Homo_sapiens.GRCh37.75_partChr1andX.gtf
Parsing annotation ...

Annotation Parsed!
Cromosomes found in annotation file: 1,X
Time to parse annotation: 0:00:00.957582

Number of CPU:s 4
Start parsing the variants ...

VariantConsumer-2: Starting!
VariantConsumer-3: Starting!
VariantConsumer-4: Starting!
Traceback (most recent call last):
  File "/Users/timothyh/home/bin/arch/genmod-0.9.7/scripts/run_genmod.py", line 241, in <module>
    main()
  File "/Users/timothyh/home/bin/arch/genmod-0.9.7/scripts/run_genmod.py", line 203, in main
    var_parser.parse()
  File "build/bdist.macosx-10.8-intel/egg/genmod/vcf/vcf_parser.py", line 127, in parse
TypeError: __init__() takes exactly 4 arguments (6 given)
VariantConsumer-5: Starting!
VariantConsumer-6: Starting!
VariantConsumer-7: Starting!
VariantConsumer-8: Starting!
VariantPrinter-9: starting!
Process VariantPrinter-9:
Traceback (most recent call last):
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "build/bdist.macosx-10.8-intel/egg/genmod/utils/variant_printer.py", line 39, in run
    next_result = self.task_queue.get()
  File "<string>", line 2, in get
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/managers.py", line 759, in _callmethod
    kind, result = conn.recv()
EOFError

[moonso]

Sorry about that, I've made a mistake during an upgrade. Fix it asap and get back to you.

[moonso]

Hi,

this should be solved now!

[tzhughes]

Tested and confirmed fixed.