Ignore tmp directory.
Switch from YAML::Tiny to YAML for data (not config). YAML::Tiny could not read all data it wrote.
Bin reads separately for each strand.
Get read peaks separately for each strand.
Merge read peaks separately for each strand.
Revert "Merge read peaks separately for each strand".

This reverts commit 58a04960f8ecd841067eac0cd4563b71f3bee8a8.
Merge read peaks separately for each strand.
Summarise read peaks separately for each strand.
Typo.
Run peak HMM separately for each strand.
Join HMM bins separately for each strand.
Get 3' ends separately for each strand.
Only count read 2s on same strand as 3' end. That is, ignore read 2s that definitely aren't associated with this 3' end.
Merge branch 'two-stranded-peak-calling'.

Previously peak calling was done in a combined way, but we know the strand of each second read, so it can be done separately for each strand.