├── Debug ├── makefile ├── objects.mk ├── sources.mk └── src │ ├── Barcodes.d │ ├── Barcodes.o │ ├── Eval_GT.d │ ├── Eval_GT.o │ ├── IO │ ├── FastaParser.d │ ├── FastaParser.o │ ├── FastqParser.d │ ├── FastqParser.o │ └── subdir.mk │ ├── Parse_biobank.d │ ├── Parse_biobank.o │ ├── Scan_fastq.d │ ├── Scan_fastq.o │ ├── Schatz_example.d │ ├── Schatz_example.o │ ├── Steph.d │ ├── Steph.o │ ├── SubsamplePac.d │ ├── SubsamplePac.o │ ├── Tools │ ├── Filter_length.d │ ├── Filter_length.o │ ├── Nucleotide_distribution.d │ ├── Nucleotide_distribution.o │ ├── Summarize_length.d │ ├── Summarize_length.o │ └── subdir.mk │ ├── combine_assemblies.d │ ├── combine_assemblies.o │ ├── manipulate_fasta.d │ ├── manipulate_fasta.o │ ├── merge.d │ ├── merge.o │ ├── merge_assembly.d │ ├── merge_assembly.o │ ├── norm_table.d │ ├── norm_table.o │ ├── parse_kraken.d │ ├── parse_kraken.o │ ├── sample_tree.d │ ├── sample_tree.o │ ├── strange_annotaiton.d │ ├── strange_annotaiton.o │ └── subdir.mk ├── LICENSE ├── README.md ├── SVCollector.sh ├── simul ├── demo.sh ├── fitcurve.R └── popsim.pl ├── src ├── SVCollector.cpp ├── Select_samples.cpp └── Select_samples.h └── vis └── SVCollectorPlot.R /Debug/makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/makefile -------------------------------------------------------------------------------- /Debug/objects.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/objects.mk -------------------------------------------------------------------------------- /Debug/sources.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/sources.mk -------------------------------------------------------------------------------- /Debug/src/Barcodes.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Barcodes.d -------------------------------------------------------------------------------- /Debug/src/Barcodes.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Barcodes.o -------------------------------------------------------------------------------- /Debug/src/Eval_GT.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Eval_GT.d -------------------------------------------------------------------------------- /Debug/src/Eval_GT.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Eval_GT.o -------------------------------------------------------------------------------- /Debug/src/IO/FastaParser.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/IO/FastaParser.d -------------------------------------------------------------------------------- /Debug/src/IO/FastaParser.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/IO/FastaParser.o -------------------------------------------------------------------------------- /Debug/src/IO/FastqParser.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/IO/FastqParser.d -------------------------------------------------------------------------------- /Debug/src/IO/FastqParser.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/IO/FastqParser.o -------------------------------------------------------------------------------- /Debug/src/IO/subdir.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/IO/subdir.mk -------------------------------------------------------------------------------- /Debug/src/Parse_biobank.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Parse_biobank.d -------------------------------------------------------------------------------- /Debug/src/Parse_biobank.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Parse_biobank.o -------------------------------------------------------------------------------- /Debug/src/Scan_fastq.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Scan_fastq.d -------------------------------------------------------------------------------- /Debug/src/Scan_fastq.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Scan_fastq.o -------------------------------------------------------------------------------- /Debug/src/Schatz_example.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Schatz_example.d -------------------------------------------------------------------------------- /Debug/src/Schatz_example.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Schatz_example.o -------------------------------------------------------------------------------- /Debug/src/Steph.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Steph.d -------------------------------------------------------------------------------- /Debug/src/Steph.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Steph.o -------------------------------------------------------------------------------- /Debug/src/SubsamplePac.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/SubsamplePac.d -------------------------------------------------------------------------------- /Debug/src/SubsamplePac.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/SubsamplePac.o -------------------------------------------------------------------------------- /Debug/src/Tools/Filter_length.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Filter_length.d -------------------------------------------------------------------------------- /Debug/src/Tools/Filter_length.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Filter_length.o -------------------------------------------------------------------------------- /Debug/src/Tools/Nucleotide_distribution.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Nucleotide_distribution.d -------------------------------------------------------------------------------- /Debug/src/Tools/Nucleotide_distribution.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Nucleotide_distribution.o -------------------------------------------------------------------------------- /Debug/src/Tools/Summarize_length.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Summarize_length.d -------------------------------------------------------------------------------- /Debug/src/Tools/Summarize_length.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/Summarize_length.o -------------------------------------------------------------------------------- /Debug/src/Tools/subdir.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/Tools/subdir.mk -------------------------------------------------------------------------------- /Debug/src/combine_assemblies.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/combine_assemblies.d -------------------------------------------------------------------------------- /Debug/src/combine_assemblies.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/combine_assemblies.o -------------------------------------------------------------------------------- /Debug/src/manipulate_fasta.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/manipulate_fasta.d -------------------------------------------------------------------------------- /Debug/src/manipulate_fasta.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/manipulate_fasta.o -------------------------------------------------------------------------------- /Debug/src/merge.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/merge.d -------------------------------------------------------------------------------- /Debug/src/merge.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/merge.o -------------------------------------------------------------------------------- /Debug/src/merge_assembly.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/merge_assembly.d -------------------------------------------------------------------------------- /Debug/src/merge_assembly.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/merge_assembly.o -------------------------------------------------------------------------------- /Debug/src/norm_table.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/norm_table.d -------------------------------------------------------------------------------- /Debug/src/norm_table.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/norm_table.o -------------------------------------------------------------------------------- /Debug/src/parse_kraken.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/parse_kraken.d -------------------------------------------------------------------------------- /Debug/src/parse_kraken.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/parse_kraken.o -------------------------------------------------------------------------------- /Debug/src/sample_tree.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/sample_tree.d -------------------------------------------------------------------------------- /Debug/src/sample_tree.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/sample_tree.o -------------------------------------------------------------------------------- /Debug/src/strange_annotaiton.d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/strange_annotaiton.d -------------------------------------------------------------------------------- /Debug/src/strange_annotaiton.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/strange_annotaiton.o -------------------------------------------------------------------------------- /Debug/src/subdir.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/Debug/src/subdir.mk -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/README.md -------------------------------------------------------------------------------- /SVCollector.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/SVCollector.sh -------------------------------------------------------------------------------- /simul/demo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/simul/demo.sh -------------------------------------------------------------------------------- /simul/fitcurve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/simul/fitcurve.R -------------------------------------------------------------------------------- /simul/popsim.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/simul/popsim.pl -------------------------------------------------------------------------------- /src/SVCollector.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/src/SVCollector.cpp -------------------------------------------------------------------------------- /src/Select_samples.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/src/Select_samples.cpp -------------------------------------------------------------------------------- /src/Select_samples.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/src/Select_samples.h -------------------------------------------------------------------------------- /vis/SVCollectorPlot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fritzsedlazeck/SVCollector/HEAD/vis/SVCollectorPlot.R --------------------------------------------------------------------------------