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Improvements to indel calling.#1679

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jkbonfield wants to merge 31 commits into
samtools:developfrom
jkbonfield:indel-tweak-jkb1
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Improvements to indel calling.#1679
jkbonfield wants to merge 31 commits into
samtools:developfrom
jkbonfield:indel-tweak-jkb1

Add a check for end of reference when indel calling.

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