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Initial code review of changes for hg38 alt contigs #63

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@rnpandya rnpandya commented Dec 9, 2015

You can generate test files with tests/alttestgen.py (test.fa, test_alts.txt, test.sam).

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Compile on Linux
42717f9
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Merge branch 'master' into alts
ce53004 
Conflicts:
	SNAPLib/BaseAligner.cpp
	SNAPLib/Genome.h
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