Hi Samtools Team -
Thanks for delivering the samtools 1.x release! I've come across one issue
working with cram files in this release, which is that idxstats will run on
cram files, but doesn't actually provide read counts.
This can be reproduced in today's master
(b7c4b4d05154887ec8587165c6da505aad024f52) :
"""
# from samtools directory:
$ samtools idxstats test/mpileup/ce#5b.bam
CHROMOSOME_I 15072423 1 0
CHROMOSOME_II 15279345 1 0
CHROMOSOME_III 13783700 1 0
CHROMOSOME_IV 17493793 1 0
CHROMOSOME_V 20924149 3 0
* 0 0 0
$ samtools idxstats test/mpileup/ce#5b.cram
CHROMOSOME_I 15072423 0 0
CHROMOSOME_II 15279345 0 0
CHROMOSOME_III 13783700 0 0
CHROMOSOME_IV 17493793 0 0
CHROMOSOME_V 20924149 0 0
* 0 0 139886584375224
"""
Should this function still be available with the new indices or is this going
to be a legacy utility?
Thanks,
-Chris
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