├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── aligner.py ├── bowtie2.py ├── bwamem.py ├── feature_table.py ├── fit.py ├── hisat2.py ├── images └── qtip_flow.png ├── mapq.py ├── metamat.py ├── model_fam.py ├── predictions.py ├── qtip ├── roc.py ├── scripts ├── .gitignore ├── README.md ├── fastq_interleave.py └── mason_convert.py ├── snap.py ├── software ├── README.md ├── bowtie2 │ ├── .gitignore │ ├── Makefile │ └── Makefile.from_github ├── bwa │ ├── .gitignore │ ├── Makefile │ ├── README.md │ ├── bwa_conc_flags_0.7.15.patch │ └── patch_outline.txt ├── hisat2 │ ├── .gitignore │ └── Makefile.from_github ├── mason │ ├── .gitignore │ └── Makefile └── snap │ ├── .gitignore │ ├── Makefile │ ├── Makefile.linux │ ├── Makefile.mac │ ├── README.md │ ├── snap_features_patch.diff │ ├── snap_patch.diff │ └── test │ ├── .gitignore │ ├── README.md │ └── test1.sh ├── src ├── .gitignore ├── Makefile ├── NEWS.md ├── README.md ├── align.cpp ├── align.h ├── ds.h ├── edit_xscript.h ├── 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