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bioinfologics / sdg

Sequence Distance Graph framework: graph + reads + mapping + analysis
MIT License
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Possible overflow in ws.ls() #128

Open jonwright99 opened 4 years ago

jonwright99 commented 4 years ago

Running ws.ls() on a wheat size dataset gives a truncated output without the kmer counter details;

Correct output (not wheat); SDG Workspace SequenceDistanceGraph SDG: 1024254 nodes, 1349282 links Distance Graphs: 0 Paired Read Datastores: 1 Paired Reads Datastore pe: 168907918 reads Paired Reads Mapper: 0 mapped reads, 0 unmapped Linked Read Datastores: 0 Long Read Datastores: 0 Kmer Count Datastores: 1 KmerCounter pcrf_reads: index with 260546793 31-mers Counts: 2 sdg: 543119471 total 31-mers pcrf_reads: 28252065131 total 31-mers

Output for wheat; SDG Workspace SequenceDistanceGraph SDG: 19116679 nodes, 26420231 links Distance Graphs: 0 Paired Read Datastores: 1 Paired Reads Datastore ei_pe: 3390968002 reads Paired Reads Mapper: 0 mapped reads, 0 unmapped Linked Read Datastores: 0 Long Read Datastores: 0 Kmer Count Datastores: 1

jonwright99 commented 4 years ago

I think this is a bug in the code. 'Kmer Count Datastores' uses the same value as 'Paired Read Datastores' in workspace::ls()