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Catch when cannot determine insert size data #60

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martinghunt
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If no proper mapped pairs are found, then cannot determine the insert size. Previously, it would have an assertion fail. This changes it to print a warning to stderr and finish the run (with no assemblies carried out and nothing to report).

@martinghunt martinghunt merged commit 973d792 into sanger-pathogens:master Apr 21, 2016
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