remove unnecessary include statements
add interface for parallel sorting in bamsort
change default sbs buffer size in bamtofastq
use posix based input in bammarkduplicates2
use posix based input in bamtofastq
add input buffer size parameter
bump libmaus version
add parameter for filtering by tag id in resetAlignment
add input buffer size parameter in bammarkduplicates2
simplify
- fix resetAlignment function
- correct auxfilter key in bamcollate2
- add keys for controlling auxilliary tag resetting in bamreset
- refactor aux tag list parsing
bump libmaus version
set mapping quality to zero when resetting BAM entries
bump libmaus version
bump version after adding parameter of tags to keep during BAM resetting
improve the documentation for bamsort
mark bamcollate as deprecated in the documentation
print warning message that bamcollate is deprecated when it is run
remove debug message