[med-svn] [Git][med-team/seqan2][master] 21 commits: New upstream version 2.5.0~rc1+dfsg

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / seqan2


Commits:
b506e8bb by Michael R. Crusoe at 2024-08-03T13:24:55+02:00
New upstream version 2.5.0~rc1+dfsg
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841d856a by Michael R. Crusoe at 2024-08-16T13:03:51+02:00
New upstream version 2.5.0~rc2+dfsg
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b2c20078 by Michael R. Crusoe at 2024-11-23T00:18:12+01:00
New upstream version 2.5.0~rc3+dfsg
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65483141 by Michael R. Crusoe at 2026-01-07T12:10:47+01:00
d/rules: remove workaround for archs we no longer build for.

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39565071 by Michael R. Crusoe at 2026-01-07T12:11:06+01:00
d/control: drop build-dep on fakeroot

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b7a95db9 by Michael R. Crusoe at 2026-01-07T12:15:56+01:00
New upstream version

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9a96552e by Michael R. Crusoe at 2026-01-07T12:16:00+01:00
New upstream version 2.5.1
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0250cca0 by Michael R. Crusoe at 2026-01-07T12:16:40+01:00
Update upstream source from tag 'upstream/2.5.1'

Update to upstream version '2.5.1'
with Debian dir 495852babd0a85dd7867a6aa04d5d98570e67eac
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3b0eaf33 by Michael R. Crusoe at 2026-01-07T12:16:42+01:00
Standards-Version: 4.7.3 (routine-update)

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a1fddb2e by Michael R. Crusoe at 2026-01-07T12:17:05+01:00
debputy lint --auto-fix (routine-update)

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7366d7b2 by Michael R. Crusoe at 2026-01-07T12:35:23+01:00
d/patches: many patches upstreamed and removed.

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cdc3048a by Michael R. Crusoe at 2026-01-07T12:35:27+01:00
d/rules: configure with -DALIGN_SIMD_TEST=FALSE as per upstream

to avoid compiling a 256+ level template in debug mode which takes up too much memory.

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b32dc425 by Michael R. Crusoe at 2026-01-07T12:35:27+01:00
debian/libseqan2-dev.docs: README.rst→README.md

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50a3c9ee by Michael R. Crusoe at 2026-01-07T12:38:07+01:00
d/rules: According to upstream, solution_online_search_finder.cpp works again, so stop deleting that test

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bef35786 by Enrico Seiler at 2026-01-07T12:40:30+01:00
d/control: remove unneeded deps

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2218bfb2 by Enrico Seiler at 2026-01-07T12:42:53+01:00
d/rules: strip path from seqan-apps, special options for salsa

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6778bb8d by Enrico Seiler at 2026-01-07T12:43:58+01:00
d/salsa-ci.yml: Skip arm64 crossbuild and reprotest, add env var for use by d/rules

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e6dc6148 by Enrico Seiler at 2026-01-07T12:44:30+01:00
d/patches: refresh patches

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4fca4860 by Enrico Seiler at 2026-01-07T12:51:54+01:00
d/patches: remove forwarded patches

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22a01ab3 by Michael R. Crusoe at 2026-01-07T12:51:54+01:00
d/upstream/metadata: link to upstream's git repo

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f5d29b02 by Michael R. Crusoe at 2026-01-07T13:04:50+01:00
d/rules: re-enable maximal parallel building.

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2239 changed files:

- + CHANGELOG.md
- − CHANGELOG.rst
- CMakeLists.txt
- CONTRIBUTING.rst → CONTRIBUTING.md
- LICENSE
- + README.md
- − README.rst
- apps/CMakeLists.txt
- apps/alf/CMakeLists.txt
- apps/alf/LICENSE
- apps/alf/README
- apps/alf/alf.cpp
- apps/bs_tools/CMakeLists.txt
- apps/bs_tools/LICENSE
- apps/bs_tools/README
- apps/bs_tools/README.bisar
- apps/bs_tools/README.casbar
- apps/bs_tools/bisar.cpp
- apps/bs_tools/bisar.h
- apps/bs_tools/bisar_base.h
- apps/bs_tools/bisar_score.h
- apps/bs_tools/bisar_score_data.h
- apps/bs_tools/casbar.cpp
- apps/bs_tools/casbar.h
- apps/bs_tools/casbar_alphabets.h
- apps/bs_tools/casbar_calling.h
- apps/bs_tools/casbar_consensus_realign.h
- apps/bs_tools/casbar_realignment.h
- apps/bs_tools/casbar_score.h
- apps/bs_tools/casbar_score_data.h
- apps/bs_tools/casbar_util.h
- apps/bs_tools/four2three.cpp
- apps/bs_tools/four2three.h
- apps/bs_tools/tests/run_tests.py
- apps/dfi/CMakeLists.txt
- apps/dfi/LICENSE
- apps/dfi/README
- apps/dfi/dfi.cpp
- apps/dfi/tests/run_tests.py
- apps/fiona/CMakeLists.txt
- apps/fiona/LICENSE
- apps/fiona/README
- apps/fiona/compute_gain.cpp
- apps/fiona/error_rate_from_sam.cpp
- apps/fiona/fiona.cpp
- apps/fiona/index_qgram_parallel.h
- apps/fiona/tests/run_tests.py
- apps/fx_tools/CMakeLists.txt
- apps/fx_tools/LICENSE
- apps/fx_tools/fx_bam_coverage.cpp
- apps/fx_tools/fx_fastq_stats.cpp
- apps/gustaf/CMakeLists.txt
- apps/gustaf/LICENSE
- apps/gustaf/README
- apps/gustaf/README.rst
- apps/gustaf/create_stellarmatches_from_file.h
- apps/gustaf/gustaf.cpp
- apps/gustaf/gustaf_matepairs.h
- apps/gustaf/join_mates.cpp
- apps/gustaf/msplazer.h
- apps/gustaf/msplazer_algorithms.h
- apps/gustaf/msplazer_main.h
- apps/gustaf/msplazer_out.h
- apps/gustaf/msplazer_parse_options.h
- apps/gustaf/stellar_routines.h
- apps/gustaf/tests/run_tests.py
- apps/insegt/CMakeLists.txt
- apps/insegt/LICENSE
- apps/insegt/README
- apps/insegt/base.h
- apps/insegt/create_gff.h
- apps/insegt/fusion.h
- apps/insegt/insegt.cpp
- apps/insegt/overlap_module.h
- apps/insegt/tests/run_tests.py
- apps/mason2/CMakeLists.txt
- apps/mason2/LICENSE
- apps/mason2/README
- apps/mason2/README.mason_frag_sequencing
- apps/mason2/README.mason_genome
- apps/mason2/README.mason_materializer
- apps/mason2/README.mason_methylation
- + apps/mason2/README.mason_methylation.levels.md
- apps/mason2/README.mason_simulator
- apps/mason2/README.mason_splicing
- apps/mason2/README.mason_variator
- apps/mason2/external_split_merge.cpp
- apps/mason2/external_split_merge.h
- apps/mason2/fragment_generation.h
- apps/mason2/genomic_variants.cpp
- apps/mason2/genomic_variants.h
- apps/mason2/individual_genome.h
- apps/mason2/mason_frag_sequencing.cpp
- apps/mason2/mason_genome.cpp
- apps/mason2/mason_materializer.cpp
- apps/mason2/mason_methylation.cpp
- apps/mason2/mason_options.cpp
- apps/mason2/mason_options.h
- apps/mason2/mason_simulator.cpp
- apps/mason2/mason_splicing.cpp
- apps/mason2/mason_tests.cpp
- apps/mason2/mason_types.h
- apps/mason2/mason_variator.cpp
- apps/mason2/methylation_levels.cpp
- apps/mason2/methylation_levels.h
- apps/mason2/omp_wrapper.h
- apps/mason2/sequencing.h
- apps/mason2/simulate_454.cpp
- apps/mason2/simulate_base.cpp
- apps/mason2/simulate_genome.cpp
- apps/mason2/simulate_genome.h
- apps/mason2/simulate_illumina.cpp
- apps/mason2/simulate_sanger.cpp
- apps/mason2/tests/generate_outputs.sh
- − apps/mason2/tests/genome.test1.fa
- − apps/mason2/tests/genome.test2.fa
- apps/mason2/tests/adeno_virus.fa → apps/mason2/tests/input/adeno_virus.fa
- apps/mason2/tests/adeno_virus.fa.fai → apps/mason2/tests/input/adeno_virus.fa.fai
- apps/mason2/tests/random.fasta → apps/mason2/tests/input/random.fasta
- apps/mason2/tests/random.fasta.fai → apps/mason2/tests/input/random.fasta.fai
- apps/mason2/tests/genome.test1.fasta → apps/mason2/tests/libc++/genome.test1.fasta
- apps/mason2/tests/genome.test1.stderr → apps/mason2/tests/libc++/genome.test1.stderr
- apps/mason2/tests/genome.test1.stdout → apps/mason2/tests/libc++/genome.test1.stdout
- + apps/mason2/tests/libc++/genome.test2.fasta
- apps/mason2/tests/genome.test2.stderr → apps/mason2/tests/libc++/genome.test2.stderr
- apps/mason2/tests/genome.test2.stdout → apps/mason2/tests/libc++/genome.test2.stdout
- apps/mason2/tests/materializer.random_var1.stderr → apps/mason2/tests/libc++/materializer.random_var1.stderr
- apps/mason2/tests/materializer.random_var1.stdout → apps/mason2/tests/libc++/materializer.random_var1.stdout
- apps/mason2/tests/materializer.random_var2.stderr → apps/mason2/tests/libc++/materializer.random_var2.stderr
- apps/mason2/tests/materializer.random_var2.stdout → apps/mason2/tests/libc++/materializer.random_var2.stdout
- apps/mason2/tests/methylation.test2.stderr → apps/mason2/tests/libc++/methylation.test1.stderr
- apps/mason2/tests/methylation.test1.stdout → apps/mason2/tests/libc++/methylation.test1.stdout
- + apps/mason2/tests/libc++/random_meth1.fasta
- apps/mason2/tests/random_meth1.fasta.fai → apps/mason2/tests/libc++/random_meth1.fasta.fai
- + apps/mason2/tests/libc++/random_var1.fasta
- + apps/mason2/tests/libc++/random_var1.vcf
- + apps/mason2/tests/libc++/random_var1.vcf.stderr
- apps/mason2/tests/random_var1.vcf.stdout → apps/mason2/tests/libc++/random_var1.vcf.stdout
- apps/mason2/tests/random_var10.vcf.stdout → apps/mason2/tests/libc++/random_var10.fasta
- apps/mason2/tests/random_var10.vcf → apps/mason2/tests/libc++/random_var10.vcf
- apps/mason2/tests/random_var10.vcf.stderr → apps/mason2/tests/libc++/random_var10.vcf.stderr
- apps/mason2/tests/random_var2.vcf.stdout → apps/mason2/tests/libc++/random_var10.vcf.stdout
- + apps/mason2/tests/libc++/random_var1_bp.txt
- + apps/mason2/tests/libc++/random_var1_meth.fasta
- + apps/mason2/tests/libc++/random_var2.fasta
- + apps/mason2/tests/libc++/random_var2.vcf
- + apps/mason2/tests/libc++/random_var2.vcf.stderr
- apps/mason2/tests/random_var3.vcf.stdout → apps/mason2/tests/libc++/random_var2.vcf.stdout
- + apps/mason2/tests/libc++/random_var2_bp.txt
- + apps/mason2/tests/libc++/random_var2_meth.fasta
- + apps/mason2/tests/libc++/random_var3.fasta
- + apps/mason2/tests/libc++/random_var3.vcf
- + apps/mason2/tests/libc++/random_var3.vcf.stderr
- apps/mason2/tests/random_var9.vcf.stdout → apps/mason2/tests/libc++/random_var3.vcf.stdout
- + apps/mason2/tests/libc++/random_var3_bp.txt
- + apps/mason2/tests/libc++/random_var9.fasta
- + apps/mason2/tests/libc++/random_var9.vcf
- + apps/mason2/tests/libc++/random_var9.vcf.stderr
- apps/mason2/tests/simulator.out1.stdout → apps/mason2/tests/libc++/random_var9.vcf.stdout
- + apps/mason2/tests/libc++/simulator.left1.fq
- + apps/mason2/tests/libc++/simulator.left2.fq
- + apps/mason2/tests/libc++/simulator.left3.fa
- + apps/mason2/tests/libc++/simulator.left4.fa
- + apps/mason2/tests/libc++/simulator.left5.fq
- + apps/mason2/tests/libc++/simulator.left6.fq
- + apps/mason2/tests/libc++/simulator.left7.fa
- + apps/mason2/tests/libc++/simulator.left8.fq
- + apps/mason2/tests/libc++/simulator.out1.sam
- + apps/mason2/tests/libc++/simulator.out1.stderr
- apps/mason2/tests/simulator.out2.stdout → apps/mason2/tests/libc++/simulator.out1.stdout
- + apps/mason2/tests/libc++/simulator.out2.sam
- + apps/mason2/tests/libc++/simulator.out2.stderr
- apps/mason2/tests/simulator.out3.stdout → apps/mason2/tests/libc++/simulator.out2.stdout
- + apps/mason2/tests/libc++/simulator.out3.stderr
- apps/mason2/tests/simulator.out4.stdout → apps/mason2/tests/libc++/simulator.out3.stdout
- + apps/mason2/tests/libc++/simulator.out4.sam
- + apps/mason2/tests/libc++/simulator.out4.stderr
- apps/mason2/tests/simulator.out5.stdout → apps/mason2/tests/libc++/simulator.out4.stdout
- + apps/mason2/tests/libc++/simulator.out5.stderr
- apps/mason2/tests/simulator.out6.stdout → apps/mason2/tests/libc++/simulator.out5.stdout
- + apps/mason2/tests/libc++/simulator.out6.stderr
- apps/mason2/tests/simulator.out7.stdout → apps/mason2/tests/libc++/simulator.out6.stdout
- + apps/mason2/tests/libc++/simulator.out7.sam
- + apps/mason2/tests/libc++/simulator.out7.stderr
- apps/mason2/tests/simulator.out8.stdout → apps/mason2/tests/libc++/simulator.out7.stdout
- + apps/mason2/tests/libc++/simulator.out8.sam
- + apps/mason2/tests/libc++/simulator.out8.stderr
- + apps/mason2/tests/libc++/simulator.out8.stdout
- + apps/mason2/tests/libc++/simulator.right1.fq
- + apps/mason2/tests/libc++/simulator.right2.fq
- + apps/mason2/tests/libc++/simulator.right3.fa
- + apps/mason2/tests/libc++/simulator.right5.fq
- + apps/mason2/tests/libc++/simulator.right6.fq
- apps/mason2/tests/genome.test2.fasta → apps/mason2/tests/libstdc++/genome.test1.fasta
- + apps/mason2/tests/libstdc++/genome.test1.stderr
- + apps/mason2/tests/libstdc++/genome.test1.stdout
- + apps/mason2/tests/libstdc++/genome.test2.fasta
- + apps/mason2/tests/libstdc++/genome.test2.stderr
- + apps/mason2/tests/libstdc++/genome.test2.stdout
- + apps/mason2/tests/libstdc++/materializer.random_var1.stderr
- + apps/mason2/tests/libstdc++/materializer.random_var1.stdout
- + apps/mason2/tests/libstdc++/materializer.random_var2.stderr
- + apps/mason2/tests/libstdc++/materializer.random_var2.stdout
- + apps/mason2/tests/libstdc++/methylation.test1.stderr
- + apps/mason2/tests/libstdc++/methylation.test1.stdout
- apps/mason2/tests/random_meth1.fasta → apps/mason2/tests/libstdc++/random_meth1.fasta
- + apps/mason2/tests/libstdc++/random_meth1.fasta.fai
- apps/mason2/tests/random_var1.fasta → apps/mason2/tests/libstdc++/random_var1.fasta
- apps/mason2/tests/random_var1.vcf → apps/mason2/tests/libstdc++/random_var1.vcf
- apps/mason2/tests/random_var1.vcf.stderr → apps/mason2/tests/libstdc++/random_var1.vcf.stderr
- + apps/mason2/tests/libstdc++/random_var1.vcf.stdout
- + apps/mason2/tests/libstdc++/random_var10.fasta
- + apps/mason2/tests/libstdc++/random_var10.vcf
- + apps/mason2/tests/libstdc++/random_var10.vcf.stderr
- + apps/mason2/tests/libstdc++/random_var10.vcf.stdout
- apps/mason2/tests/random_var1_bp.txt → apps/mason2/tests/libstdc++/random_var1_bp.txt
- apps/mason2/tests/random_var1_meth.fasta → apps/mason2/tests/libstdc++/random_var1_meth.fasta
- apps/mason2/tests/random_var2.fasta → apps/mason2/tests/libstdc++/random_var2.fasta
- apps/mason2/tests/random_var2.vcf → apps/mason2/tests/libstdc++/random_var2.vcf
- apps/mason2/tests/random_var2.vcf.stderr → apps/mason2/tests/libstdc++/random_var2.vcf.stderr
- + apps/mason2/tests/libstdc++/random_var2.vcf.stdout
- apps/mason2/tests/random_var2_bp.txt → apps/mason2/tests/libstdc++/random_var2_bp.txt
- apps/mason2/tests/random_var2_meth.fasta → apps/mason2/tests/libstdc++/random_var2_meth.fasta
- apps/mason2/tests/random_var3.fasta → apps/mason2/tests/libstdc++/random_var3.fasta
- apps/mason2/tests/random_var3.vcf → apps/mason2/tests/libstdc++/random_var3.vcf
- apps/mason2/tests/random_var3.vcf.stderr → apps/mason2/tests/libstdc++/random_var3.vcf.stderr
- + apps/mason2/tests/libstdc++/random_var3.vcf.stdout
- apps/mason2/tests/random_var3_bp.txt → apps/mason2/tests/libstdc++/random_var3_bp.txt
- apps/mason2/tests/random_var9.fasta → apps/mason2/tests/libstdc++/random_var9.fasta
- apps/mason2/tests/random_var9.vcf → apps/mason2/tests/libstdc++/random_var9.vcf
- apps/mason2/tests/random_var9.vcf.stderr → apps/mason2/tests/libstdc++/random_var9.vcf.stderr
- + apps/mason2/tests/libstdc++/random_var9.vcf.stdout
- + apps/mason2/tests/libstdc++/simulator.left1.fq
- + apps/mason2/tests/libstdc++/simulator.left2.fq
- apps/mason2/tests/simulator.left3.fa → apps/mason2/tests/libstdc++/simulator.left3.fa
- apps/mason2/tests/simulator.left4.fa → apps/mason2/tests/libstdc++/simulator.left4.fa
- + apps/mason2/tests/libstdc++/simulator.left5.fq
- + apps/mason2/tests/libstdc++/simulator.left6.fq
- + apps/mason2/tests/libstdc++/simulator.left7.fa
- + apps/mason2/tests/libstdc++/simulator.left8.fq
- + apps/mason2/tests/libstdc++/simulator.out1.sam
- apps/mason2/tests/simulator.out1.stderr → apps/mason2/tests/libstdc++/simulator.out1.stderr
- + apps/mason2/tests/libstdc++/simulator.out1.stdout
- + apps/mason2/tests/libstdc++/simulator.out2.sam
- apps/mason2/tests/simulator.out2.stderr → apps/mason2/tests/libstdc++/simulator.out2.stderr
- + apps/mason2/tests/libstdc++/simulator.out2.stdout
- apps/mason2/tests/simulator.out3.stderr → apps/mason2/tests/libstdc++/simulator.out3.stderr
- + apps/mason2/tests/libstdc++/simulator.out3.stdout
- + apps/mason2/tests/libstdc++/simulator.out4.sam
- apps/mason2/tests/simulator.out4.stderr → apps/mason2/tests/libstdc++/simulator.out4.stderr
- + apps/mason2/tests/libstdc++/simulator.out4.stdout
- apps/mason2/tests/simulator.out5.stderr → apps/mason2/tests/libstdc++/simulator.out5.stderr
- + apps/mason2/tests/libstdc++/simulator.out5.stdout
- apps/mason2/tests/simulator.out6.stderr → apps/mason2/tests/libstdc++/simulator.out6.stderr
- + apps/mason2/tests/libstdc++/simulator.out6.stdout
- + apps/mason2/tests/libstdc++/simulator.out7.sam
- apps/mason2/tests/simulator.out7.stderr → apps/mason2/tests/libstdc++/simulator.out7.stderr
- + apps/mason2/tests/libstdc++/simulator.out7.stdout
- + apps/mason2/tests/libstdc++/simulator.out8.sam
- apps/mason2/tests/simulator.out8.stderr → apps/mason2/tests/libstdc++/simulator.out8.stderr
- + apps/mason2/tests/libstdc++/simulator.out8.stdout
- + apps/mason2/tests/libstdc++/simulator.right1.fq
- + apps/mason2/tests/libstdc++/simulator.right2.fq
- apps/mason2/tests/simulator.right3.fa → apps/mason2/tests/libstdc++/simulator.right3.fa
- + apps/mason2/tests/libstdc++/simulator.right5.fq
- + apps/mason2/tests/libstdc++/simulator.right6.fq
- − apps/mason2/tests/mason_genome.test1.stderr
- − apps/mason2/tests/mason_genome.test2.stderr
- − apps/mason2/tests/random.fa
- − apps/mason2/tests/random_meth1.fa
- − apps/mason2/tests/random_var1.fa
- − apps/mason2/tests/random_var10.fa
- − apps/mason2/tests/random_var10.fasta
- − apps/mason2/tests/random_var1_meth.fa
- − apps/mason2/tests/random_var2.fa
- − apps/mason2/tests/random_var2_meth.fa
- − apps/mason2/tests/random_var3.fa
- − apps/mason2/tests/random_var9.fa
- apps/mason2/tests/run_tests.py
- − apps/mason2/tests/simulator.left1.fq
- − apps/mason2/tests/simulator.left2.fq
- − apps/mason2/tests/simulator.left5.fq
- − apps/mason2/tests/simulator.left6.fq
- − apps/mason2/tests/simulator.left7.fa
- − apps/mason2/tests/simulator.left8.fq
- − apps/mason2/tests/simulator.out1.sam
- − apps/mason2/tests/simulator.out2.sam
- − apps/mason2/tests/simulator.out4.sam
- − apps/mason2/tests/simulator.out5.sam
- − apps/mason2/tests/simulator.out6.sam
- − apps/mason2/tests/simulator.out7.sam
- − apps/mason2/tests/simulator.out8.sam
- − apps/mason2/tests/simulator.right1.fq
- − apps/mason2/tests/simulator.right2.fq
- − apps/mason2/tests/simulator.right5.fq
- − apps/mason2/tests/simulator.right6.fq
- − apps/mason2/tests/variants.var10.tsv
- apps/mason2/variation_size_tsv.h
- apps/mason2/vcf_materialization.cpp
- apps/mason2/vcf_materialization.h
- apps/micro_razers/CMakeLists.txt
- apps/micro_razers/LICENSE
- apps/micro_razers/README
- apps/micro_razers/micro_razers.cpp
- apps/micro_razers/outputFormat.h
- apps/micro_razers/tests/run_tests.py
- apps/ngs_roi/CMakeLists.txt
- apps/ngs_roi/R/README
- apps/ngs_roi/R/ngsroi/DESCRIPTION
- apps/ngs_roi/README
- apps/ngs_roi/bam2roi.cpp
- apps/ngs_roi/bam2roi.h
- apps/ngs_roi/png_canvas.h
- apps/ngs_roi/project_interval.cpp
- apps/ngs_roi/project_interval.h
- apps/ngs_roi/project_spliced.cpp
- apps/ngs_roi/project_spliced.h
- apps/ngs_roi/record_ext.h
- apps/ngs_roi/roi_builder.cpp
- apps/ngs_roi/roi_builder.h
- apps/ngs_roi/roi_feature_projection.cpp
- apps/ngs_roi/roi_plot_thumbnails.cpp
- apps/ngs_roi/tests/run_tests.py
- apps/ngs_roi/tool_shed/README
- apps/ngs_roi/tool_shed/argparse26.py
- apps/ngs_roi/tool_shed/bam2roi.ctd
- apps/ngs_roi/tool_shed/ctd2galaxy.py
- apps/ngs_roi/tool_shed/ngs_roi/app.py
- apps/ngs_roi/tool_shed/ngs_roi/argparse.py
- apps/ngs_roi/tool_shed/ngs_roi/io.py
- apps/ngs_roi/tool_shed/roi_details.py
- apps/ngs_roi/tool_shed/roi_feature_projection.ctd
- apps/ngs_roi/tool_shed/roi_intersect.ctd
- apps/ngs_roi/tool_shed/roi_plot_thumbnails.ctd
- apps/ngs_roi/tool_shed/roi_plot_thumbnails.py
- apps/ngs_roi/tool_shed/roi_report.py
- apps/ngs_roi/tool_shed/roi_table.py
- apps/ngs_roi/tool_shed/rois.py
- apps/pair_align/CMakeLists.txt
- apps/pair_align/LICENSE
- apps/pair_align/lib/pair_align_global.cpp
- apps/pair_align/lib/pair_align_lcs.cpp
- apps/pair_align/lib/pair_align_lib.cpp
- apps/pair_align/lib/pair_align_lib.h
- apps/pair_align/lib/pair_align_local.cpp
- apps/pair_align/pair_align.cpp
- apps/pair_align/tests/VTML200I
- apps/pair_align/tests/run_tests.py
- apps/param_chooser/CMakeLists.txt
- apps/param_chooser/LICENSE
- apps/param_chooser/param_chooser.cpp
- apps/param_chooser/test_param_chooser.cpp
- apps/rabema/CMakeLists.txt
- apps/rabema/COPYING
- apps/rabema/LICENSE
- apps/rabema/README
- apps/rabema/curve_smoothing.h
- apps/rabema/do_search.cpp
- apps/rabema/doc/real_world_workflow.svg
- apps/rabema/doc/simulation_workflow.svg
- apps/rabema/find_hamming_simple_ext.h
- apps/rabema/find_myers_ukkonen_ext.h
- apps/rabema/find_myers_ukkonen_reads.h
- apps/rabema/io_gsi.h
- apps/rabema/prepare_sam.cpp
- apps/rabema/rabema.cpp
- apps/rabema/rabema.h
- apps/rabema/rabema_build_gold_standard.cpp
- apps/rabema/rabema_evaluate.cpp
- apps/rabema/rabema_stats.h
- apps/rabema/ref_id_mapping.h
- apps/rabema/sorting.h
- apps/rabema/tests/run_tests.py
- apps/razers/CMakeLists.txt
- apps/razers/LICENSE
- apps/razers/README
- apps/razers/gapped_params/dat2cpp.py
- apps/razers/outputFormat.h
- apps/razers/paramChooser.h
- apps/razers/param_tabs.cpp
- apps/razers/param_tabs.h
- apps/razers/razers.cpp
- apps/razers/razers.h
- apps/razers/razers_matepairs.h
- apps/razers/razers_spliced.h
- apps/razers/readSimulator.h
- apps/razers/tests/pe-adeno-reads36_2-id-of2.eland
- apps/razers/tests/run_tests.py
- apps/razers3/CMakeLists.txt
- apps/razers3/LICENSE
- apps/razers3/README
- apps/razers3/compPHSens.cpp
- apps/razers3/job_queue.h
- apps/razers3/outputFormat.h
- apps/razers3/parallel_job_queue.h
- apps/razers3/parallel_misc.h
- apps/razers3/parallel_store.h
- apps/razers3/paramChooser.h
- apps/razers3/param_tabs.cpp
- apps/razers3/param_tabs.h
- apps/razers3/profile_timeline.h
- apps/razers3/quality2prob.cpp
- apps/razers3/razers.cpp
- apps/razers3/razers.h
- apps/razers3/razers_match_filter.h
- apps/razers3/razers_matepairs.h
- apps/razers3/razers_matepairs_parallel.h
- apps/razers3/razers_paired_match_filter.h
- apps/razers3/razers_parallel.h
- apps/razers3/razers_window.h
- apps/razers3/readSimulator.h
- apps/razers3/simulate_reads.cpp
- apps/razers3/tests/pe-adeno-reads100_2-i97-tc1.razers
- apps/razers3/tests/pe-adeno-reads100_2-i98-tc1.razers
- apps/razers3/tests/pe-adeno-reads100_2-i99-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-f-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i92-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i93-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i94-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i95-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i96-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-i97-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-of0-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-of5-tc0.afg
- apps/razers3/tests/pe-adeno-reads36_2-of5-tc1.afg
- apps/razers3/tests/pe-adeno-reads36_2-r-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-so0-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-so1-tc1.razers
- apps/razers3/tests/pe-adeno-reads36_2-tc1.razers
- apps/razers3/tests/run_tests.py
- apps/razers3/tests/run_tests_sequential.py
- apps/razers3/tests/se-adeno-reads36_1-of5-tc0.afg
- apps/razers3/tests/se-adeno-reads36_1-of5-tc1.afg
- apps/rep_sep/CMakeLists.txt
- apps/rep_sep/LICENSE
- apps/rep_sep/assembly_parser.h
- apps/rep_sep/column_scanner.h
- apps/rep_sep/rep_sep.cpp
- apps/rep_sep/rgraph.h
- apps/rep_sep/rgraph_base.h
- apps/rep_sep/rgraph_construction.h
- apps/rep_sep/rgraph_heuristics.h
- apps/rep_sep/rgraph_score.h
- apps/rep_sep/utils.h
- apps/sak/CMakeLists.txt
- apps/sak/LICENSE
- apps/sak/sak.cpp
- apps/sak/tests/run_tests.py
- apps/sam2matrix/CMakeLists.txt
- apps/sam2matrix/LICENSE
- apps/sam2matrix/sam2matrix.cpp
- apps/sam2matrix/tests/run_tests.py
- apps/samcat/CMakeLists.txt
- apps/samcat/LICENSE
- apps/samcat/samcat.cpp
- apps/samcat/tests/run_tests.py
- apps/searchjoin/CMakeLists.txt
- apps/searchjoin/LICENSE
- apps/searchjoin/README
- apps/searchjoin/db.h
- apps/searchjoin/finder.h
- apps/searchjoin/join.cpp
- apps/searchjoin/search.cpp
- apps/searchjoin/tests/run_tests.py
- apps/searchjoin/verifier.h
- apps/searchjoin/writer.h
- apps/seqan_tcoffee/CMakeLists.txt
- apps/seqan_tcoffee/LICENSE
- apps/seqan_tcoffee/README
- apps/seqan_tcoffee/seqan_tcoffee.cpp
- apps/seqan_tcoffee/tests/VTML200I
- apps/seqan_tcoffee/tests/run_tests.py
- apps/seqcons2/CMakeLists.txt
- apps/seqcons2/LICENSE
- apps/seqcons2/seqcons.cpp
- apps/seqcons2/seqcons_app.cpp
- apps/seqcons2/seqcons_app.h
- apps/seqcons2/seqcons_options.cpp
- apps/seqcons2/seqcons_options.h
- apps/seqcons2/tests/run_tests.py
- apps/sgip/CMakeLists.txt
- apps/sgip/LICENSE
- apps/sgip/sgip.cpp
- apps/sgip/sgip.h
- apps/sgip/sgip_base.h
- apps/sgip/sgip_output.h
- apps/sgip/tests/run_tests.py
- apps/snp_store/CMakeLists.txt
- apps/snp_store/LICENSE
- apps/snp_store/README
- apps/snp_store/snp_store.cpp
- apps/snp_store/snp_store.h
- apps/snp_store/tests/run_tests.py
- apps/splazers/CMakeLists.txt
- apps/splazers/LICENSE
- apps/splazers/README
- apps/splazers/outputFormat.h
- apps/splazers/paramChooser.h
- apps/splazers/razers.h
- apps/splazers/razers_matepairs.h
- apps/splazers/razers_parallel.h
- apps/splazers/razers_spliced.h
- apps/splazers/readSimulator.h
- apps/splazers/splazers.cpp
- apps/splazers/tests/run_tests.py
- apps/stellar/CMakeLists.txt
- apps/stellar/LICENSE
- apps/stellar/README
- apps/stellar/stellar.cpp
- apps/stellar/stellar.h
- apps/stellar/stellar_extension.h
- apps/stellar/stellar_output.h
- apps/stellar/stellar_types.h
- apps/stellar/tests/run_tests.py
- apps/tree_recon/CMakeLists.txt
- apps/tree_recon/LICENSE
- apps/tree_recon/tests/run_tests.py
- apps/tree_recon/tree_recon.cpp
- apps/yara/CMakeLists.txt
- apps/yara/LICENSE
- apps/yara/README.rst
- apps/yara/basic_alphabet.h
- apps/yara/bits_bucket.h
- apps/yara/bits_context.h
- apps/yara/bits_hits.h
- apps/yara/bits_matches.h
- apps/yara/bits_reads.h
- apps/yara/bits_seeds.h
- apps/yara/file_pair.h
- apps/yara/file_prefetched.h
- apps/yara/find_extender.h
- apps/yara/find_verifier.h
- apps/yara/index_fm.h
- apps/yara/indexer.cpp
- apps/yara/mapper.cpp
- apps/yara/mapper.h
- apps/yara/mapper_aligner.h
- apps/yara/mapper_classifier.h
- apps/yara/mapper_collector.h
- apps/yara/mapper_extender.h
- apps/yara/mapper_filter.h
- apps/yara/mapper_ranker.h
- apps/yara/mapper_verifier.h
- apps/yara/mapper_writer.h
- apps/yara/misc_options.h
- apps/yara/misc_tags.h
- apps/yara/misc_timer.h
- apps/yara/misc_types.h
- apps/yara/store_seqs.h
- + apps/yara/tests/gold/adeno-reads_1.as.rec.t1.sam
- + apps/yara/tests/gold/adeno-reads_1.as.tag.t1.sam
- + apps/yara/tests/gold/adeno-reads_1.rec.t1.sam
- + apps/yara/tests/gold/adeno-reads_1.tag.t1.sam
- apps/yara/tests/run_tests.py
- debian/changelog
- debian/control
- debian/libseqan2-dev.docs
- − debian/patches/ctdVersion.patch
- − debian/patches/fix-version_check-test
- − debian/patches/fix_manpage_formatting.patch
- − debian/patches/fix_python3_tests
- − debian/patches/ia64_yield
- − debian/patches/install_fiona_illumina
- − debian/patches/no-unaligned-access.patch
- − debian/patches/python3
- debian/patches/series
- − debian/patches/skip-seqan-revision
- debian/patches/skip-some-apps-on-some-archs
- − debian/patches/spelling
- debian/patches/tweak_readmes
- debian/rules
- debian/salsa-ci.yml
- debian/upstream/metadata
- demos/CMakeLists.txt
- demos/LICENSE
- demos/blast/blast_in_lowlevel.cpp
- demos/dox/align/align.cpp
- demos/dox/align/compute_alignment_stats.cpp
- demos/dox/align/gaps_example.cpp
- demos/dox/align/global_alignment_banded.cpp
- demos/dox/align/global_alignment_unbanded.cpp
- + demos/dox/align/global_alignment_unbanded_execution_policy.cpp
- + demos/dox/align/global_alignment_unbanded_execution_policy.cpp.stdout
- + demos/dox/align/global_alignment_unbanded_score_execution_policy_parallel.cpp
- + demos/dox/align/global_alignment_unbanded_score_execution_policy_parallel.cpp.stdout
- + demos/dox/align/global_alignment_unbanded_score_execution_policy_wavefront.cpp
- + demos/dox/align/global_alignment_unbanded_score_execution_policy_wavefront.cpp.stdout
- demos/dox/align/integrate_align.cpp
- + demos/dox/align/local_alignment_unbanded_execution_policy.cpp
- + demos/dox/align/local_alignment_unbanded_execution_policy.cpp.stdout
- + demos/dox/align/local_alignment_unbanded_score_execution_policy_parallel.cpp
- + demos/dox/align/local_alignment_unbanded_score_execution_policy_parallel.cpp.stdout
- + demos/dox/align/local_alignment_unbanded_score_execution_policy_wavefront.cpp
- + demos/dox/align/local_alignment_unbanded_score_execution_policy_wavefront.cpp.stdout
- demos/dox/align_extend/extend_alignment.cpp
- demos/dox/align_profile/profile_seq_frac_score.cpp
- demos/dox/align_profile/profile_seq_score.cpp
- demos/dox/align_split/split_alignment.cpp
- demos/dox/arg_parse/argument_parser.cpp
- demos/dox/bam_io/bam_file_in.cpp
- demos/dox/bam_io/bam_tags_dict.cpp
- demos/dox/basic/enable_if.cpp
- demos/dox/basic/metaprogramming_control.cpp
- demos/dox/basic/metaprogramming_logic.cpp
- demos/dox/basic/metaprogramming_math.cpp
- demos/dox/basic/metaprogramming_switch.cpp
- demos/dox/basic/simple_type_construction.cpp
- demos/dox/basic/zip_iterator.cpp
- demos/dox/bed_io/UNUSED_bed_stream_read.cpp
- demos/dox/consensus/consensus_alignment.cpp
- demos/dox/find/finder_aho_corasick.cpp
- demos/dox/find/finder_index.cpp
- demos/dox/find/finder_online.cpp
- demos/dox/gff_io/UNUSED_gff_stream_read.cpp
- demos/dox/graph_algorithms/all_pairs_shortest_path.cpp
- demos/dox/graph_algorithms/bellman_ford_algorithm.cpp
- demos/dox/graph_algorithms/breadth_first_search.cpp
- demos/dox/graph_algorithms/dag_shortest_path.cpp
- demos/dox/graph_algorithms/depth_first_search.cpp
- demos/dox/graph_algorithms/dijkstra.cpp
- demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp
- demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp
- demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp
- demos/dox/graph_algorithms/kruskals_algorithm.cpp
- demos/dox/graph_algorithms/longest_common_subsequence.cpp
- demos/dox/graph_algorithms/longest_increasing_subsequence.cpp
- demos/dox/graph_algorithms/prims_algorithm.cpp
- demos/dox/graph_algorithms/strongly_connected_components.cpp
- demos/dox/graph_algorithms/topological_sort.cpp
- demos/dox/graph_algorithms/transitive_closure.cpp
- demos/dox/graph_align/graph_align.cpp
- demos/dox/graph_types/graph_algo_dijkstra.cpp
- demos/dox/index/UNUSED_shape.cpp
- demos/dox/index/UNUSED_shape_hash.cpp
- demos/dox/index/UNUSED_shape_hash_next.cpp
- demos/dox/index/begin_atEnd_representative.cpp
- demos/dox/index/begin_atEnd_representative_bottomUp.cpp
- demos/dox/index/begin_range_goDown_representative_repLength.cpp
- demos/dox/index/counting.cpp
- demos/dox/index/find_repeats.cpp
- demos/dox/index/finder.cpp
- demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
- demos/dox/index/iterator.cpp
- demos/dox/index/iterator_short.cpp
- demos/dox/index/length_countSequences.cpp
- demos/dox/index/maxrepeats.cpp
- demos/dox/index/mummy.cpp
- demos/dox/index/mums.cpp
- demos/dox/index/node_predicate.cpp
- demos/dox/index/open_save.cpp
- demos/dox/index/shape_hash_init.cpp
- demos/dox/index/sufarray.cpp
- demos/dox/index/supermaxrepeats.cpp
- demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
- demos/dox/misc/enumerate_strings.cpp
- demos/dox/misc/get_terminal_size.cpp
- demos/dox/misc/interval_tree_example.cpp
- demos/dox/misc/name_store_cache.cpp
- demos/dox/modifier/cyclic_shape.cpp
- demos/dox/modifier/cyclic_shape_snippets.cpp
- demos/dox/modifier/modified_string.cpp
- demos/dox/modifier/modified_string_mod_view.cpp
- demos/dox/modifier/modified_string_nested.cpp
- demos/dox/parallel/queue_example.cpp
- demos/dox/parallel/splitter_example.cpp
- demos/dox/pipe/pool_sorter.cpp
- demos/dox/score/score.cpp
- demos/dox/seeds/seeds_add_seed.cpp
- demos/dox/seeds/seeds_chaining.cpp
- demos/dox/seeds/seeds_extension.cpp
- demos/dox/seq_io/fai_index_example.cpp
- demos/dox/sequence/UNUSED_infix.cpp
- demos/dox/sequence/UNUSED_prefix.cpp
- demos/dox/sequence/UNUSED_suffix.cpp
- demos/dox/sequence/container_view_zip.cpp
- demos/dox/sequence/segment.cpp
- demos/dox/sequence/string.cpp
- demos/dox/sequence/string2.cpp
- demos/dox/sequence/stringset.cpp
- demos/dox/statistics/build_markov_model.cpp
- demos/dox/statistics/load_markov_model.cpp
- demos/dox/store/store_example.cpp
- demos/dox/stream/lexical_cast.cpp
- demos/howto/align_gaps_clipping.cpp
- demos/howto/custom_file_endings.cpp
- demos/howto/efficiently_import_sequences.cpp
- demos/howto/filter_similar_sequences.cpp
- demos/howto/scores/init_score.cpp
- demos/howto/scores/load_score.cpp
- demos/howto/using_zip_iterator.cpp
- demos/tabix_io/tabix_vcf.cpp
- demos/tutorial/a_first_example/base.cpp
- demos/tutorial/a_first_example/basic_code.cpp
- demos/tutorial/a_first_example/basic_code_detailed.cpp
- demos/tutorial/a_first_example/code_encapsulation.cpp
- demos/tutorial/a_first_example/example_tags_for_print.cpp
- demos/tutorial/a_first_example/final_result.cpp
- demos/tutorial/a_first_example/solution_1.cpp
- demos/tutorial/a_first_example/solution_2.cpp
- demos/tutorial/a_first_example/solution_3.cpp
- demos/tutorial/a_first_example/solution_4.cpp
- demos/tutorial/a_first_example/solution_4_templateSubclassing.cpp
- demos/tutorial/a_first_example/solution_5.cpp
- demos/tutorial/a_first_example/solution_6.cpp
- demos/tutorial/alignment/align.cpp
- demos/tutorial/alignment/align_assignment1.cpp
- demos/tutorial/alignment/graph.cpp
- demos/tutorial/alignment/graph_assignment1.cpp
- demos/tutorial/alignment/scoring_scheme_affine_dgs.cpp
- demos/tutorial/alignment/scoring_scheme_matrix.cpp
- demos/tutorial/alignment/scoring_scheme_simple.cpp
- demos/tutorial/alphabets/assignment_1.cpp
- demos/tutorial/alphabets/assignment_1_solution.cpp
- demos/tutorial/alphabets/example_bitsPerValue.cpp
- demos/tutorial/alphabets/example_ordValue.cpp
- demos/tutorial/alphabets/example_size.cpp
- demos/tutorial/background_and_motivation/example.cpp
- demos/tutorial/basic_techniques/base.cpp
- demos/tutorial/basics/allocator.cpp
- demos/tutorial/basics/base.cpp
- demos/tutorial/basics/show_alphabets.cpp
- demos/tutorial/basics/strings.cpp
- demos/tutorial/bed_io/base.cpp
- demos/tutorial/bed_io/example1.cpp
- demos/tutorial/bed_io/solution1.cpp
- demos/tutorial/bed_io/solution2.cpp
- demos/tutorial/bed_io/solution3.cpp
- demos/tutorial/blast_io/read_assignment.cpp
- demos/tutorial/blast_io/write_assignment.cpp
- demos/tutorial/blast_io/write_assignment.m0
- demos/tutorial/blast_io/write_assignment.m9
- demos/tutorial/consensus_alignment/with_positions.cpp
- demos/tutorial/consensus_alignment/without_positions.cpp
- − demos/tutorial/file_io_overview/example.sam
- demos/tutorial/file_io_overview/example1.cpp
- demos/tutorial/file_io_overview/solution1.cpp
- demos/tutorial/file_io_overview/solution2.cpp
- demos/tutorial/file_io_overview/solution3.cpp
- demos/tutorial/fragment_store/access_aligned_reads.cpp
- demos/tutorial/fragment_store/access_aligned_reads2.cpp
- demos/tutorial/fragment_store/base.cpp
- demos/tutorial/fragment_store/display_aligned_reads.cpp
- demos/tutorial/generic_programming/example_hashing.cpp
- demos/tutorial/generic_programming/template_subclassing.cpp
- demos/tutorial/genome_annotations/assignment_1_hint.cpp
- demos/tutorial/genome_annotations/assignment_1_solution.cpp
- demos/tutorial/genome_annotations/assignment_2_solution.cpp
- demos/tutorial/genome_annotations/assignment_3_solution.cpp
- demos/tutorial/genome_annotations/assignment_4_solution.cpp
- demos/tutorial/genome_annotations/base.cpp
- demos/tutorial/gff_and_gtf_io/base.cpp
- demos/tutorial/gff_and_gtf_io/example1.cpp
- demos/tutorial/gff_and_gtf_io/example2.cpp
- demos/tutorial/gff_and_gtf_io/solution1.cpp
- demos/tutorial/gff_and_gtf_io/solution2.cpp
- demos/tutorial/gff_and_gtf_io/solution3.cpp
- demos/tutorial/graph/graph_algo_scc.cpp
- demos/tutorial/graph/graph_dijkstra.cpp
- demos/tutorial/graph/graph_hmm.cpp
- demos/tutorial/graph/solution_1.cpp
- demos/tutorial/index_iterators/index_assignment1.cpp
- demos/tutorial/index_iterators/index_assignment2.cpp
- demos/tutorial/index_iterators/index_bidirectional_search.cpp
- demos/tutorial/index_iterators/index_preorder.cpp
- demos/tutorial/index_iterators/index_property_maps.cpp
- demos/tutorial/index_iterators/index_search.cpp
- demos/tutorial/index_iterators/index_search2.cpp
- demos/tutorial/index_iterators/iterator_assignment2.cpp
- demos/tutorial/index_iterators/iterator_solution1.cpp
- demos/tutorial/index_iterators/iterator_solution2.cpp
- demos/tutorial/index_iterators/iterator_solution3.cpp
- demos/tutorial/indexed_fasta_io/base.cpp
- demos/tutorial/indexed_fasta_io/solution1.cpp
- demos/tutorial/indexed_fasta_io/solution2.cpp
- demos/tutorial/indices/assignment_1.cpp
- demos/tutorial/indices/assignment_2.cpp
- demos/tutorial/indices/base.cpp
- demos/tutorial/indices/find2_index_approx.cpp
- demos/tutorial/indices/fm_index.cpp
- demos/tutorial/iterators/assignment_1.cpp
- demos/tutorial/iterators/assignment_1_solution.cpp
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- tests/store/test_store.cpp
- tests/store/test_store_io.h
- tests/store/test_store_io_bam.h
- tests/stream/CMakeLists.txt
- tests/stream/test_stream.cpp
- tests/stream/test_stream_file_stream.h
- tests/stream/test_stream_generic.h
- tests/stream/test_stream_lexical_cast.h
- tests/stream/test_stream_tokenization.h
- tests/stream/test_stream_virtual_stream.h
- tests/stream/test_stream_write.h
- tests/swift_local/CMakeLists.txt
- tests/swift_local/test_find_swift.cpp
- tests/tabix_io/CMakeLists.txt
- tests/tabix_io/test_tabix_io.cpp
- tests/tabix_io/test_tabix_io.h
- tests/translation/CMakeLists.txt
- tests/translation/test_translation.cpp
- tests/translation/test_translation.h
- tests/ucsc_io/CMakeLists.txt
- tests/ucsc_io/test_ucsc_io.cpp
- tests/vcf_io/CMakeLists.txt
- tests/vcf_io/test_vcf_io.cpp
- tests/vcf_io/test_vcf_io.h
- util/bin/adjust_copyright_years.sh
- util/bin/auto_build.py
- util/bin/dddoc.py
- util/bin/demo_checker.py
- util/bin/dox.py
- util/bin/fixgcov.py
- + util/bin/link_check.sh
- util/bin/profile2pdf.py
- util/bin/pyclangcheck.py
- util/bin/skel.py
- + util/bump_app_versions.sh
- util/cmake/CheckSymbolExists.cmake
- util/cmake/FeatureSummary.cmake
- util/cmake/FindBZip2.cmake
- util/cmake/FindGitInfo.cmake
- util/cmake/FindSDE.cmake
- util/cmake/FindTBB/FindTBB.cmake
- util/cmake/FindTBB/README
- util/cmake/FindUmesimd.cmake
- util/cmake/GetCurrentDate.cmake
- util/cmake/GetCurrentDate.cpp
- util/cmake/README
- util/cmake/SeqAnBuildSystem.cmake
- util/cmake/SeqAnConsistentFPFlags.cmake
- util/cmake/SeqAnContribs.cmake
- util/cmake/SeqAnCtdSetup.cmake
- util/cmake/SeqAnSimdUtility.cmake
- util/cmake/SeqAnUsabilityAnalyzer.cmake
- util/cmake/SetCPackSystemName.cmake
- util/cmake/ctd/COPYRIGHT
- util/cmake/ctd/LICENSE
- util/cmake/ctd/mimetypes.xml
- util/cmake/package.cmake
- + util/cmake/seqan-config-version.cmake
- util/cmake/seqan-config.cmake
- util/ctd2galaxy.py
- util/headers/header_bsd.txt
- util/headers/header_gpl3.txt
- util/linux_binary_tests.sh
- util/makefile_project/Makefile.rules
- util/makefile_project/src/main.cpp
- util/pkgconfig/seqan.pc.in
- util/ports/science/coinor-liblemon/Portfile
- util/ports/science/seqan-apps/Portfile
- util/ports/science/seqan/Portfile
- util/py_lib/CMakeLists.txt
- util/py_lib/seqan/LICENSE
- util/py_lib/seqan/app_tests.py
- util/py_lib/seqan/auto_build.py
- util/py_lib/seqan/fixgcov/__init__.py
- util/py_lib/seqan/fixgcov/app.py
- util/py_lib/seqan/paths.py
- util/py_lib/seqan/pyclangcheck/__init__.py
- util/py_lib/seqan/pyclangcheck/app.py
- util/py_lib/seqan/pyclangcheck/rules.py
- util/py_lib/seqan/pyclangcheck/simple_checks.py
- util/py_lib/seqan/pyclangcheck/suppressions.py
- util/py_lib/seqan/pyclangcheck/violations.py
- util/py_lib/seqan/seqan.html
- util/py_lib/seqan/skel.py
- util/raw_cmake_project/CMakeLists.txt
- util/raw_cmake_project/src/CMakeLists.txt
- util/raw_cmake_project/src/main.cpp
- util/skel/app_template/CMakeLists.txt
- util/skel/app_template/LICENSE
- util/skel/app_template/app.cpp
- util/skel/app_tests_template/run_tests.py
- util/skel/demo_template/demo.cpp
- util/skel/header_template/header.h
- util/skel/header_template/library_header.h
- util/skel/module_template/header.h
- util/skel/module_template/module.h
- util/skel/repository_template/CMakeLists.txt
- util/skel/repository_template/apps_CMakeLists.txt
- util/skel/repository_template/demos_CMakeLists.txt
- util/skel/repository_template/tests_CMakeLists.txt
- util/skel/test_template/CMakeLists.txt
- util/skel/test_template/test.cpp
- util/skel/test_template/test.h
- − util/travis/linux-cibuild.cmake
- − util/travis/linux-cibuild.sh
- util/valgrind/python.supp
- util/valgrind/seqan.supp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/seqan2/-/compare/82435d23d935d552b865e4a33d6439b6ad94c8ee...f5d29b0235262d65271a5570f1fe6474bdbfeb93

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View it on GitLab: https://salsa.debian.org/med-team/seqan2/-/compare/82435d23d935d552b865e4a33d6439b6ad94c8ee...f5d29b0235262d65271a5570f1fe6474bdbfeb93
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