Updated runtime files
Oh boy
Added --min-read-end-match and --min-border options to filter out reads prior to allelotyping
Testing
Merged with upstream changes
adding test cases for ReadContainer
Added dummy checks for alignment filters. Moves alignment filters from ReadContainer to separate file
adding more tests for readcontainer. moved code to get samples to there from common.cpp
adding tests of different input file tpes
Filled in unit tests for alignment filters
Merge branch 'master' of https://github.com/mgymrek/lobstr-code
Added --min-bp-before-indel option to filter aligned reads whose indels occur too close to the read ends
Incorportated pull request comments. Added files for Needleman-Wunsch alignment that has no end-gap penalty for the reference sequence
Incorportated pull request comments. Added files for Needleman-Wunsch alignment that has no end-gap penalty for the reference sequence
Added unit tests for new NW functions
adding test files so make distcheck works
Merge branch 'master' of https://github.com/mgymrek/lobstr-code
Fixed CIGAROP error
Merge pull request #29 from tfwillems/master

Alignment Checks
changing docs saying --rg-library to --rg-lib