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bin/consolidate_vcfs.pl
bin/core-only.pl
bin/extract_snvs_metaalign.pl
bin/filter-positions.pl
bin/filter-stats.pl
bin/filter_unique_basepairs.pl
bin/filterVcf.pl
bin/find-positions-used.pl
bin/find-repeats.pl
bin/positions2phyloviz.pl
bin/positions2snv_alignment.pl
bin/positions2snv_invariant_alignment.pl
bin/rearrange_snv_matrix.pl
bin/ref_stats.pl
bin/reporter.pl
bin/snv_matrix.pl
bin/tsvToVcf.pl
bin/vcf2snv_alignment.pl
bin/verify_excess_coverage.pl
bin/verify_low_depth.pl
bin/verify_mapping_quality.pl
lib/CompareFiles.pm
lib/CorePositions.pm
lib/InvalidPositions.pm
lib/PositionsTable.pm
lib/Streaming.pm
Makefile.PL
MANIFEST
README.md
t/tree/expected/5/phylogeneticTree.txt
t/tree/expected/5/revisedMatrix.csv
t/tree/expected/2/phylogeneticTree.txt
t/tree/expected/6/phylogeneticTree.txt
t/tree/expected/6/revisedMatrix.csv
t/tree/expected/3/phylogeneticTree.txt
t/tree/expected/4/phylogeneticTree.txt
t/tree/expected/4/revisedMatrix.csv
t/tree/expected/1/phylogeneticTree.txt
t/tree/expected/1/revisedMatrix.csv
t/tree/input/snv_align.phy
t/tree/input/matrix.csv
t/tree/input/snv_align.phy_phyml_tree.txt
t/rearrange_snv_matrix.t
t/consolidate_vcfs.t
t/filter_snv_density.t
t/matrix/output/snv_align-7.phy.out
t/matrix/output/snv_align-12.phy.out
t/matrix/output/snv_align-10.phy.out
t/matrix/output/snv_align-8.phy.out
t/matrix/output/snv_align-6.phy.out
t/matrix/output/snv_align-9.phy.out
t/matrix/output/snv_align-11.phy.out
t/matrix/output/snv_align-3.phy.out
t/matrix/output/snv_align-1.phy.out
t/matrix/output/snv_align-4.phy.out
t/matrix/output/snv_align-13.phy.out
t/matrix/output/snv_align-5.phy.out
t/matrix/output/snv_align-2.phy.out
t/matrix/input/snv_align-12.phy
t/matrix/input/snv_align-5.phy
t/matrix/input/snv_align-11.phy
t/matrix/input/snv_align-9.phy
t/matrix/input/snv_align-7.phy
t/matrix/input/snv_align-10.phy
t/matrix/input/snv_align-6.phy
t/matrix/input/snv_align-8.phy
t/matrix/input/snv_align-1.phy
t/matrix/input/snv_align-3.phy
t/matrix/input/snv_align-2.phy
t/matrix/input/snv_align-4.phy
t/matrix/input/snv_align-13.phy
t/variant_calls.t
t/verify_excess_coverage.t
t/mapping/output/output_9.txt
t/mapping/input/sample3.bam.bai
t/mapping/input/sample1.bam.bai
t/mapping/input/sample4.bam.bai
t/mapping/input/draft_reference/sample1.bam
t/mapping/input/sample1.bam
t/mapping/input/sample3.bam
t/mapping/input/sample4.bam
t/mapping/input/sample2.bam.bai
t/mapping/input/sample5.bam
t/mapping/input/sample2.bam
t/find_positions_used_data/8/output/expected_out
t/find_positions_used_data/8/input/test.gff
t/find_positions_used_data/8/input/reference.fasta
t/find_positions_used_data/8/input/bad_pos.tsv
t/find_positions_used_data/7/output/expected_out
t/find_positions_used_data/7/input/test.gff
t/find_positions_used_data/7/input/reference.fasta
t/find_positions_used_data/7/input/bad_pos.tsv
t/find_positions_used_data/5/output/expected_out
t/find_positions_used_data/5/input/test.gff
t/find_positions_used_data/5/input/reference.fasta
t/find_positions_used_data/5/input/bad_pos.tsv
t/find_positions_used_data/2/output/expected_out
t/find_positions_used_data/2/input/test.gff
t/find_positions_used_data/2/input/reference.fasta
t/find_positions_used_data/2/input/bad_pos.tsv
t/find_positions_used_data/6/output/expected_out
t/find_positions_used_data/6/input/test.gff
t/find_positions_used_data/6/input/reference.fasta
t/find_positions_used_data/6/input/bad_pos.tsv
t/find_positions_used_data/3/output/expected_out
t/find_positions_used_data/3/input/test.gff
t/find_positions_used_data/3/input/reference.fasta
t/find_positions_used_data/3/input/bad_pos.tsv
t/find_positions_used_data/4/output/expected_out
t/find_positions_used_data/4/input/test.gff
t/find_positions_used_data/4/input/reference.fasta
t/find_positions_used_data/4/input/bad_pos.tsv
t/find_positions_used_data/1/output/expected_out
t/find_positions_used_data/1/input/test.gff
t/find_positions_used_data/1/input/reference.fasta
t/find_positions_used_data/1/input/bad_pos.tsv
t/consolidate_vcfs_input/8/output/v1.bcf.gz
t/consolidate_vcfs_input/8/output/v2.bcf.gz
t/consolidate_vcfs_input/8/description
t/consolidate_vcfs_input/8/input/v1.bam
t/consolidate_vcfs_input/8/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/8/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/8/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/8/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/8/input/v1.sam
t/consolidate_vcfs_input/8/input/v2.sam
t/consolidate_vcfs_input/8/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/8/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/8/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/8/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/8/input/v2.bam
t/consolidate_vcfs_input/18/output/v1.bcf.gz
t/consolidate_vcfs_input/18/output/v2.bcf.gz
t/consolidate_vcfs_input/18/description
t/consolidate_vcfs_input/18/input/v1.bam
t/consolidate_vcfs_input/18/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/18/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/18/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/18/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/18/input/v1.sam
t/consolidate_vcfs_input/18/input/v2.sam
t/consolidate_vcfs_input/18/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/18/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/18/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/18/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/18/input/v2.bam
t/consolidate_vcfs_input/noN.10/output/v1.bcf.gz
t/consolidate_vcfs_input/noN.10/output/v2.bcf.gz
t/consolidate_vcfs_input/noN.10/description
t/consolidate_vcfs_input/noN.10/input/v1.bam
t/consolidate_vcfs_input/noN.10/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/noN.10/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/noN.10/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/noN.10/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/noN.10/input/v1.sam
t/consolidate_vcfs_input/noN.10/input/v2.sam
t/consolidate_vcfs_input/noN.10/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/noN.10/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/noN.10/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/noN.10/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/noN.10/input/v2.bam
t/consolidate_vcfs_input/7/output/v1.bcf.gz
t/consolidate_vcfs_input/7/output/v2.bcf.gz
t/consolidate_vcfs_input/7/description
t/consolidate_vcfs_input/7/input/v1.bam
t/consolidate_vcfs_input/7/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/7/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/7/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/7/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/7/input/v1.sam
t/consolidate_vcfs_input/7/input/v2.sam
t/consolidate_vcfs_input/7/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/7/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/7/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/7/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/7/input/v2.bam
t/consolidate_vcfs_input/14/output/v1.bcf.gz
t/consolidate_vcfs_input/14/output/v2.bcf.gz
t/consolidate_vcfs_input/14/description
t/consolidate_vcfs_input/14/input/v1.bam
t/consolidate_vcfs_input/14/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/14/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/14/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/14/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/14/input/v1.sam
t/consolidate_vcfs_input/14/input/v2.sam
t/consolidate_vcfs_input/14/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/14/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/14/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/14/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/14/input/v2.bam
t/consolidate_vcfs_input/22/output/v1.bcf.gz
t/consolidate_vcfs_input/22/output/v2.bcf.gz
t/consolidate_vcfs_input/22/description
t/consolidate_vcfs_input/22/input/v1.bam
t/consolidate_vcfs_input/22/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/22/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/22/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/22/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/22/input/v1.sam
t/consolidate_vcfs_input/22/input/v2.sam
t/consolidate_vcfs_input/22/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/22/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/22/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/22/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/22/input/v2.bam
t/consolidate_vcfs_input/noN.7/output/v1.bcf.gz
t/consolidate_vcfs_input/noN.7/output/v2.bcf.gz
t/consolidate_vcfs_input/noN.7/description
t/consolidate_vcfs_input/noN.7/input/v1.bam
t/consolidate_vcfs_input/noN.7/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/noN.7/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/noN.7/input/mpileup/v2.bcf.gz
t/consolidate_vcfs_input/noN.7/input/mpileup/v2.bcf.gz.csi
t/consolidate_vcfs_input/noN.7/input/v1.sam
t/consolidate_vcfs_input/noN.7/input/v2.sam
t/consolidate_vcfs_input/noN.7/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/noN.7/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/noN.7/input/freebayes/v2.bcf.gz
t/consolidate_vcfs_input/noN.7/input/freebayes/v2.bcf.gz.csi
t/consolidate_vcfs_input/noN.7/input/v2.bam
t/consolidate_vcfs_input/28/output/v1.bcf.gz
t/consolidate_vcfs_input/28/v1.bcf.gz
t/consolidate_vcfs_input/28/description
t/consolidate_vcfs_input/28/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/28/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/28/input/freebayes/v1.bcf.gz
t/consolidate_vcfs_input/28/input/freebayes/v1.bcf.gz.csi
t/consolidate_vcfs_input/26/output/v1.bcf.gz
t/consolidate_vcfs_input/26/output/v2.bcf.gz
t/consolidate_vcfs_input/26/description
t/consolidate_vcfs_input/26/input/mpileup/v1.bcf.gz
t/consolidate_vcfs_input/26/input/mpileup/v1.vcf.gz
t/consolidate_vcfs_input/26/input/mpileup/v1.bcf.gz.csi
t/consolidate_vcfs_input/26/input/mpileup/v1.vcf.gz.csi
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t/input/3/reference.fasta.fai
t/input/3/expected_core.csv
t/input/3/reference.fasta
t/input/9/consolidate_vcf/v1.bcf.gz
t/input/9/consolidate_vcf/v1.bcf.gz.csi
t/input/9/consolidate_vcf/v2.bcf.gz
t/input/9/consolidate_vcf/v2.bcf.gz.csi
t/input/9/expected.fasta
t/input/9/description
t/input/9/expected.positions.tsv
t/input/9/reference.fasta.fai
t/input/9/expected_core.csv
t/input/9/reference.fasta
t/input/25/consolidate_vcf/v1.bcf.gz
t/input/25/consolidate_vcf/v1.bcf.gz.csi
t/input/25/consolidate_vcf/v2.bcf.gz
t/input/25/consolidate_vcf/v2.bcf.gz.csi
t/input/25/expected.fasta
t/input/25/description
t/input/25/expected.positions.tsv
t/input/25/expected_core.csv
t/input/25/reference.fasta
t/input/13/consolidate_vcf/v1.bcf.gz
t/input/13/consolidate_vcf/v1.bcf.gz.csi
t/input/13/consolidate_vcf/v2.bcf.gz
t/input/13/consolidate_vcf/v2.bcf.gz.csi
t/input/13/expected.fasta
t/input/13/description
t/input/13/expected.positions.tsv
t/input/13/reference.fasta.fai
t/input/13/expected_core.csv
t/input/13/reference.fasta
t/input/20/consolidate_vcf/v1.bcf.gz
t/input/20/consolidate_vcf/v1.bcf.gz.csi
t/input/20/consolidate_vcf/v2.bcf.gz
t/input/20/consolidate_vcf/v2.bcf.gz.csi
t/input/20/expected.fasta
t/input/20/description
t/input/20/expected.positions.tsv
t/input/20/reference.fasta.fai
t/input/20/invalid-positions.tsv
t/input/20/expected_core.csv
t/input/20/reference.fasta
t/input/4/consolidate_vcf/v1.bcf.gz