Samtools is broken since lts-2.0

[kaizhang]

Since stackage lts-2.0, at least two functions, queryLength and isReverse, are broken. queryLength always returns Nothing, while isReverse always returns True. These problems don't exist in lts-1.15 and below.

[ingolia]

Could you provide a little more to reproduce this, like a short program that grabs a single sequence from a BAM file and prints the fields, and a single-sequence .bam file?

I built the current version of samtools in a sandbox with lts-2.0 and queryLength returned the correct value, Just 100, for my test data.

[kaizhang]

https://github.com/kaizhang/samtools-test
Run stack build and then stack exec app. This will output the results of queryLength for the first 20 records. They are all Nothing in my system (Centos 7). If I switch to lts-1.15, the results are Just 32.