[untested]: split reads.to_remap by rg (for compatibility with tegetype)
first version
added SINGLE_READS_TO_REMAP for compatibility with existing data
1.2
Merge branch 'master' into matei-dev
print line numbers in xtrace
install default sigpipe handler
fix
fix file headers
more progress reports
fix
fix
updated syntax
[not functional] syntax revision, separation of lib.alu-detect.sh
rewrite of alu-detect interface. setup,add-ref,list-ref,del-ref,make-fake-ref work as expected. detect not yet
fix dealing with exmpty extra-paths
and again
more informative message
syntax & use variable fd
use sh library functions