Remove extraneous files

smangul1 · Mar 19, 2018 · 96fbb9f · 96fbb9f
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,31 +1,3 @@
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-    Read Origin Protocol is a computational protocol for profiling the 
-    composition of unmapped reads, which failed to map to the human references. 
-    ROP profiles repeats, circRNAs, gene fusions, trans-splicing events, 
-    recombined B and T cell receptors and microbial communities.
-    Copyright (c) 2016 by Serghei Mangul ([email protected]), Harry Taegyun Yang 
-    ([email protected]), Kevin Hsieh ([email protected]), and Linus Chen 
-    ([email protected]). University of California, Los Angeles (UCLA). 
-
-    Read Origin Protocol is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Read Origin Protocol is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
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                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 

diff --git a/NOTES → RELEASE.txt b/NOTES → RELEASE.txt
diff --git a/_config.yml b/_config.yml
diff --git a/example/.panfs.4f6010ac.1519323754838531000 b/example/.panfs.4f6010ac.1519323754838531000
diff --git a/example/README b/example/README
diff --git a/example/dev/SRS014476-Supragingival_plaque.fasta b/example/dev/SRS014476-Supragingival_plaque.fasta
diff --git a/example/dev/SRS014476-Supragingival_plaque.fastq b/example/dev/SRS014476-Supragingival_plaque.fastq
diff --git a/example/dev/prepare.toy.example.sh b/example/dev/prepare.toy.example.sh
diff --git a/example/unmapped.bam → example/example.bam b/example/unmapped.bam → example/example.bam
diff --git a/example/unmappedExampleFasta.fasta → example/example.fasta b/example/unmappedExampleFasta.fasta → example/example.fasta
diff --git a/example/example.fasta.gz b/example/example.fasta.gz
diff --git a/example/unmappedExample.fastq → example/example.fastq b/example/unmappedExample.fastq → example/example.fastq
diff --git a/example/example.fastq.gz b/example/example.fastq.gz
diff --git a/example/mappedReads_chr22.bam b/example/mappedReads_chr22.bam
diff --git a/example/mappedReads_chr22.bam.bai b/example/mappedReads_chr22.bam.bai
diff --git a/example/ropout/QC/rDNA_reads.txt b/example/ropout/QC/rDNA_reads.txt
diff --git a/example/ropout/QC/unmappedExample_rDNA.bam.bai b/example/ropout/QC/unmappedExample_rDNA.bam.bai
diff --git a/example/ropout/lost.human.reads/unmappedExample_genome.bam.bai b/example/ropout/lost.human.reads/unmappedExample_genome.bam.bai
diff --git a/example/ropout/lost.human.reads/unmappedExample_transcriptome.bam.bai b/example/ropout/lost.human.reads/unmappedExample_transcriptome.bam.bai
diff --git a/example/ropout/microbiome/fungi/fungi_reads.txt b/example/ropout/microbiome/fungi/fungi_reads.txt
diff --git a/example/ropout/microbiome/fungi/unmappedExample.fungi.bam b/example/ropout/microbiome/fungi/unmappedExample.fungi.bam
diff --git a/example/ropout/microbiome/fungi/unmappedExample.fungi.bam.bai b/example/ropout/microbiome/fungi/unmappedExample.fungi.bam.bai
diff --git a/example/ropout/microbiome/fungi/unmappedExample_fungi.log b/example/ropout/microbiome/fungi/unmappedExample_fungi.log
diff --git a/example/ropout/microbiome/fungi/unmappedExample_fungiFiltered.csv b/example/ropout/microbiome/fungi/unmappedExample_fungiFiltered.csv
diff --git a/example/ropout/microbiome/protozoa/protozoa_reads.txt b/example/ropout/microbiome/protozoa/protozoa_reads.txt
diff --git a/example/ropout/microbiome/protozoa/unmappedExample.protozoa.bam b/example/ropout/microbiome/protozoa/unmappedExample.protozoa.bam
diff --git a/example/ropout/microbiome/protozoa/unmappedExample.protozoa.bam.bai b/example/ropout/microbiome/protozoa/unmappedExample.protozoa.bam.bai
diff --git a/example/ropout/microbiome/protozoa/unmappedExample_protozoa.log b/example/ropout/microbiome/protozoa/unmappedExample_protozoa.log
diff --git a/example/ropout/microbiome/protozoa/unmappedExample_protozoaFiltered.csv b/example/ropout/microbiome/protozoa/unmappedExample_protozoaFiltered.csv
diff --git a/example/ropout/microbiome/viral/.panfs.336810ac.1520211164312444000 b/example/ropout/microbiome/viral/.panfs.336810ac.1520211164312444000
diff --git a/example/ropout/microbiome/viral/unmappedExample.viral.bam b/example/ropout/microbiome/viral/unmappedExample.viral.bam
diff --git a/example/ropout/microbiome/viral/unmappedExample.viral.bam.bai b/example/ropout/microbiome/viral/unmappedExample.viral.bam.bai
diff --git a/example/ropout/microbiome/viral/unmappedExample.viral.vipr.bam b/example/ropout/microbiome/viral/unmappedExample.viral.vipr.bam
diff --git a/example/ropout/microbiome/viral/unmappedExample.viral.vipr.bam.bai b/example/ropout/microbiome/viral/unmappedExample.viral.vipr.bam.bai
diff --git a/example/ropout/microbiome/viral/unmappedExample_virus.log b/example/ropout/microbiome/viral/unmappedExample_virus.log