v1.0
moved those inside alu-detect
Merge branch 'master' of /filer/alu-detect

Conflicts:
	bin/alu-detect
new alu-detect
bin-package target
tar file with version
tar file name
no .gitignore files
was missing setup
delete breakpoint evidence when ambiguous
fixes
enabled cerr from filter-mappings, add-extra-sam-fields
many more checks, sam-to-fq now binary
bug about bam input; added check that repbase libs exist
fixed bug about handling empty sam files
clarified some descriptions, thanks Orion
modified behaviour when not all RGs from headers are detected; now missing ones use default values
typo
pick pairing info with smallest stddev for each RG
typo