Relaxing the realignment constraints around the existing alignments.
Merge remote-tracking branch 'origin/master'
Fix for zero alignments.
Much faster EM parameters.
Fix to indels coverage plot.
Altering EM stuff.
Oops.
Fix.
Fix to em
Enabling blasr again.
Fix to bug.
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fixed bug, index starts from 1 now
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Adding indels
Hopefully better converging em
Fixes to EM, hopefully now all working.
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Merge remote-tracking branch 'origin/master' into em2