bugfix when PE treated as separated, undef filter considered them as single....
bugfix when PE treated as separated, undef filter considered them as single. bugfix when minimum quality score for nucleotides is 0, nucleotides with score 0 were considered as errors. -q option now takes argumens (see News file and doc)
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- configure.ac 1 addition, 1 deletionconfigure.ac
- doc/rock.pod 8 additions, 4 deletionsdoc/rock.pod
- src/CountMinSketch.hpp 14 additions, 13 deletionssrc/CountMinSketch.hpp
- src/FqBaseBackend.cpp 2 additions, 10 deletionssrc/FqBaseBackend.cpp
- src/FqMainBackend.cpp 1 addition, 1 deletionsrc/FqMainBackend.cpp
- src/FqMainBackend.h 4 additions, 3 deletionssrc/FqMainBackend.h
- src/ROCKparams.cpp 18 additions, 5 deletionssrc/ROCKparams.cpp
- src/ROCKparams.h 2 additions, 1 deletionsrc/ROCKparams.h
- src/fqreader.cpp 3 additions, 3 deletionssrc/fqreader.cpp
- src/fqreader.h 1 addition, 1 deletionsrc/fqreader.h
- src/main_utils.cpp 1 addition, 1 deletionsrc/main_utils.cpp
- src/read_utils.cpp 1 addition, 1 deletionsrc/read_utils.cpp
- src/rock.cpp 1 addition, 1 deletionsrc/rock.cpp
- src/unit_test_fqreader.cpp 17 additions, 17 deletionssrc/unit_test_fqreader.cpp
- test/Makefile.am 2 additions, 1 deletiontest/Makefile.am
- test/data/fastq.raw/klebsiella_5_1_bad_scores.fq 1 addition, 1 deletiontest/data/fastq.raw/klebsiella_5_1_bad_scores.fq
- test/data/fastq.raw/klebsiella_6_1_bad_scores.fq 24 additions, 0 deletionstest/data/fastq.raw/klebsiella_6_1_bad_scores.fq
- test/data/fastq.raw/klebsiella_6_2_bad_scores.fq 24 additions, 0 deletionstest/data/fastq.raw/klebsiella_6_2_bad_scores.fq
- test/data/iofiles.args/output_files_2_PE_separated_lenient.txt 1 addition, 0 deletions...data/iofiles.args/output_files_2_PE_separated_lenient.txt
- test/rock.sh 20 additions, 16 deletionstest/rock.sh
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