moved load_model to allow stream processing #203
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This PR closes #199 (I hope). As described in the issue, various longbow commands were failing when reading from
stdin. This PR changesload_model()to expect an openpysam.AlignmentFilerather than a stream or filename, and moves the call inside thewithstatement where the file is being read (which is almost always what happens immediately after loading a model from a BAM file).This should be okay to do, as the model is stored in the header if at all, and so
load_modelwill only consume the first piece of the stream and none of the reads.