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Replace SAMFileReader with SamReaderFactory #653

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lbergelson opened this issue Sep 14, 2016 · 0 comments · Fixed by #654
Closed

Replace SAMFileReader with SamReaderFactory #653

lbergelson opened this issue Sep 14, 2016 · 0 comments · Fixed by #654

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@lbergelson
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SAMFileReader is long deprecated and slated for destruction (see samtools/htsjdk#699). Instantiations of it should be replaced by calls to SamReaderFactory
lbergelson added a commit that referenced this issue Sep 14, 2016
@lbergelson
remove uses of SAMFileReader to fix #653
66c857c 
SAMFileReader has been deprecated for years
replacing it with a SamReader generated from a SamReaderFactory
@lbergelson lbergelson mentioned this issue Sep 14, 2016
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@lbergelson lbergelson assigned yfarjoun and unassigned yfarjoun Oct 24, 2016
lbergelson added a commit that referenced this issue Oct 24, 2016
@lbergelson
remove uses of SAMFileReader to fix #653 (#654)
558edf1 
SAMFileReader has been deprecated for years
replacing it with a SamReader generated from a SamReaderFactory
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remove uses of SAMFileReader to fix #653 broadinstitute/picard
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@yfarjoun @lbergelson