diff --git a/.gitignore b/.gitignore index fede8a6e..2919e2b1 100644 --- a/.gitignore +++ b/.gitignore @@ -99,3 +99,6 @@ pandora #portable binary build dir build_portable_executable pandora-linux-precompiled + +/archives/ +/example/out/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 977dba72..deb356ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,16 @@ project adheres to ## [Unreleased] +## [0.9.1] + +### Added +- `pandora` is now installable through `conda`; +- A script to archive the `pandora` repository with git submodules; + +### Changed +- Improved the sample example so now we can assert that the output produced is the expected one; +- Changes to the build process that enables `pandora` to be compiled in the `conda` environment; + ## [0.9.0] ### Changed @@ -97,7 +107,8 @@ from this point will have their changes meticulously documented here. - k-mer coverage underflow bug in `LocalPRG` [[#183][183]] -[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.0...HEAD +[Unreleased]: https://github.com/rmcolq/pandora/compare/0.9.1...HEAD +[0.9.1]: https://github.com/rmcolq/pandora/releases/tag/0.9.1 [0.9.0]: https://github.com/rmcolq/pandora/releases/tag/0.9.0 [0.9.0-rc2]: https://github.com/rmcolq/pandora/releases/tag/0.9.0-rc2 [0.9.0-rc1]: https://github.com/rmcolq/pandora/releases/tag/0.9.0-rc1 diff --git a/CMakeLists.txt b/CMakeLists.txt index ba25ed1f..47e29d1a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,6 +1,7 @@ cmake_minimum_required(VERSION 3.12) # required by hunter ZLIB installation # include hunter +option(HUNTER_STATUS_DEBUG "Hunter debug" OFF) # comment if does not want hunter debug on set(HUNTER_ROOT ${CMAKE_BINARY_DIR}/hunter) include("cmake/HunterGate.cmake") HunterGate( @@ -11,7 +12,7 @@ HunterGate( # project configuration set(PROJECT_NAME_STR pandora) -project(${PROJECT_NAME_STR} VERSION "0.9.0" LANGUAGES C CXX) +project(${PROJECT_NAME_STR} VERSION "0.9.1" LANGUAGES C CXX) set(ADDITIONAL_VERSION_LABELS "") configure_file( include/version.h.in ${CMAKE_BINARY_DIR}/include/version.h ) @@ -55,8 +56,13 @@ else () set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp") endif() -# static C and C++ flags -set(STATIC_C_CXX "-static-libgcc -static-libstdc++") +# always link rt +set(RT_LIBRARY "rt") + +if(NOT BIOCONDA) + # static C and C++ flags + set(STATIC_C_CXX "-static-libgcc -static-libstdc++") +endif() ######################################################################################################################## # EXTERNAL LIBS INSTALLATION @@ -92,10 +98,10 @@ set(Gtest_LIBRARIES GTest::gtest GTest::gmock_main) ######################################################################################################################## # INSTALL BOOST +set(Boost_USE_STATIC_LIBS ON) hunter_add_package(Boost COMPONENTS filesystem iostreams log serialization system thread) find_package(Boost CONFIG REQUIRED filesystem iostreams log serialization system thread) -set(BOOST_LIBRARIES Boost::filesystem Boost::iostreams Boost::log Boost::serialization Boost::system Boost::thread) -set(Boost_USE_STATIC_LIBS ON) +set(Boost_LIBRARIES Boost::filesystem Boost::iostreams Boost::log Boost::serialization Boost::system Boost::thread) ######################################################################################################################## ######################################################################################################################## # END EXTERNAL LIBS INSTALLATION @@ -148,13 +154,16 @@ add_dependencies(${PROJECT_NAME} gatb) target_link_libraries(${PROJECT_NAME} ${GATB_LIBS} - ${BOOST_LIBRARIES} + ${Boost_LIBRARIES} ${ZLIB_LIBRARY} ${CMAKE_DL_LIBS} ${STATIC_C_CXX} ${BACKWARD_LIBRARIES} ${SEQAN_LIBRARIES} + ${RT_LIBRARY} ) enable_testing() add_subdirectory(test) + +install(TARGETS ${PROJECT_NAME} RUNTIME DESTINATION bin) diff --git a/README.md b/README.md index cfc06a28..95768d16 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,7 @@ - [Hands-on toy example](#hands-on-toy-example) - [Installation](#installation) - [Precompiled portable binary](#no-installation-needed---precompiled-portable-binary) + - [Conda](#conda) - [Containers](#containers) - [Installation from source](#installation-from-source) - [Usage](#usage) @@ -78,18 +79,25 @@ In this binary, all libraries are linked statically. * **Download**: ``` - wget https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0 + wget https://github.com/rmcolq/pandora/releases/download/0.9.1/pandora-linux-precompiled-v0.9.1 ``` * **Running**: ``` -chmod +x pandora-linux-precompiled-v0.9.0 -./pandora-linux-precompiled-v0.9.0 -h +chmod +x pandora-linux-precompiled-v0.9.1 +./pandora-linux-precompiled-v0.9.1 -h ``` * **Notes**: * We provide precompiled binaries for Linux OS only; +### Conda + +To install `pandora` through `conda`, run: +``` +conda install -c bioconda pandora +``` + ### Containers [![Docker Repository on Quay](https://quay.io/repository/rmcolq/pandora/status "Docker Repository on Quay")](https://quay.io/repository/rmcolq/pandora) diff --git a/example/README.md b/example/README.md index 67a13c77..0c6781a5 100644 --- a/example/README.md +++ b/example/README.md @@ -28,18 +28,26 @@ Here we present a walkthrough of running `pandora` on a toy example. We run: ### Quick look at the output -`prgs`: contains output of `make_prg from_msa` and `pandora index`. Main files: +The output is already present in dir `out_truth`. If all went fine, the last line of the execution of the script above should be: + +``` +Example run produced the expected result +``` + +and thus the dirs `out` and `out_truth` have the same contents. + +`out/prgs`: contains output of `make_prg from_msa` and `pandora index`. Main files: * `pangenome.prg.fa`: the PRG itself; * `pangenome.prg.fa.k15.w14.idx` and `kmer_prgs`: the PRG index; * `pangenome.update_DS`: update data structures that make the PRG updateable; -`pandora_discover_out`: contains the output of `pandora discover`. Main files: +`out/pandora_discover_out`: contains the output of `pandora discover`. Main files: * `denovo_paths.txt`: describes the denovo paths found in all samples; -`updated_prgs`: contains the output of `make_prg update` and `pandora index` (on the updated PRG). +`out/updated_prgs`: contains the output of `make_prg update` and `pandora index` (on the updated PRG). The files are similar to the ones in the `prgs` folder; -`output_toy_example_no_denovo` and `output_toy_example_with_denovo`: contains the output of +`out/output_toy_example_no_denovo` and `out/output_toy_example_with_denovo`: contains the output of `pandora compare` without denovo discovery and with denovo discovery, respectively. Main files: * `pandora_multisample.matrix`: see https://github.com/rmcolq/pandora/wiki/FAQ#q-where-can-i-find-gene-presenceabsence-information ; * `pandora_multisample.vcf_ref.fa`: see https://github.com/rmcolq/pandora/wiki/FAQ#q-what-are-the-sequences-in-pandora_multisamplevcf_reffa @@ -50,7 +58,7 @@ The files are similar to the ones in the `prgs` folder; **No denovo** -Taking a quick look at an excerpt of `output_toy_example_no_denovo/pandora_multisample_genotyped.vcf` +Taking a quick look at an excerpt of `out/output_toy_example_no_denovo/pandora_multisample_genotyped.vcf` (the VCF genotyped by `pandora` without denovo sequences): ``` @@ -64,7 +72,7 @@ We can see samples `toy_sample_1` and `toy_sample_2` genotype towards different **With denovo** -The VCF (`output_toy_example_with_denovo/pandora_multisample_genotyped.vcf`) has some new variants that were discovered and genotyped. For example: +The VCF (`out/output_toy_example_with_denovo/pandora_multisample_genotyped.vcf`) has some new variants that were discovered and genotyped. For example: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT toy_sample_1.100x.random.illumina toy_sample_2.100x.random.illumina @@ -73,6 +81,19 @@ GC00010897 44 . C T . . SVTYPE=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_CO GC00010897 422 . A T . . SVTYPE=SNP;GRAPHTYPE=SIMPLE GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,8:0,5:0,8:0,5:0,16:0,11:1,0:-155.867,-20.2266:135.641 0:12,0:9,0:12,0:9,0:12,0:9,0:0,1:-9.39494,-182.709:173.314 ``` +## Extra + +### Running with conda + +If you install `pandora` via `conda`: `conda install -c bioconda pandora`, +you can run this sample example by activating the `conda` environment containing `pandora` and running: + +``` +./run_pandora.sh conda +``` + +The output should be the same as using the precompiled binary. + [pandora_2020_paper]: https://www.biorxiv.org/content/10.1101/2020.11.12.380378v2 diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_covgs.txt b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_covgs.txt new file mode 100644 index 00000000..8e3fd889 --- /dev/null +++ b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_covgs.txt @@ -0,0 +1,1000 @@ +0 21 +1 0 +2 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b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.consensus.fq.gz differ diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.pangraph.gfa b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.pangraph.gfa new file mode 100644 index 00000000..843c6a0f --- /dev/null +++ b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.pangraph.gfa @@ -0,0 +1,3 @@ +H VN:Z:1.0 +S GC00006032 N FC:i:234 +S GC00010897 N FC:i:227 diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_covgs.txt b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_covgs.txt new file mode 100644 index 00000000..445a7e6d --- /dev/null +++ b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_covgs.txt @@ -0,0 +1,1000 @@ +0 21 +1 1 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 1 +10 0 +11 0 +12 1 +13 3 +14 0 +15 0 +16 1 +17 1 +18 0 +19 0 +20 0 +21 1 +22 0 +23 0 +24 0 +25 1 +26 0 +27 9 +28 1 +29 2 +30 0 +31 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00000000..e775e410 --- /dev/null +++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.pangraph.gfa @@ -0,0 +1,3 @@ +H VN:Z:1.0 +S GC00006032 N FC:i:234 +S GC00010897 N FC:i:240 diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_covgs.txt b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_covgs.txt new file mode 100644 index 00000000..a3381b36 --- /dev/null +++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_covgs.txt @@ -0,0 +1,1000 @@ +0 26 +1 1 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 1 +10 0 +11 0 +12 1 +13 3 +14 0 +15 0 +16 1 +17 1 +18 0 +19 0 +20 0 +21 1 +22 0 +23 0 +24 0 +25 1 +26 0 +27 9 +28 1 +29 2 +30 0 +31 2 +32 2 +33 0 +34 3 +35 1 +36 2 +37 0 +38 0 +39 1 +40 2 +41 0 +42 0 +43 1 +44 1 +45 0 +46 1 +47 4 +48 3 +49 2 +50 6 +51 0 +52 1 +53 1 +54 1 +55 0 +56 0 +57 0 +58 1 +59 2 +60 2 +61 3 +62 2 +63 0 +64 0 +65 0 +66 0 +67 0 +68 1 +69 0 +70 0 +71 1 +72 2 +73 1 +74 4 +75 0 +76 0 +77 1 +78 1 +79 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+-36 0 +-35 0 +-34 0 +-33 0 +-32 0 +-31 0 +-30 0 +-29 0 +-28 0 +-27 0 +-26 0 +-25 0 +-24 0 +-23 0 +-22 0 +-21 0 +-20 0 +-19 0 +-18 0 +-17 0 +-16 0 +-15 0 +-14 0 +-13 0 +-12 0 +-11 0 +-10 0 +-9 26 +-8 1 +-7 2 +-6 90 +-5 0 +-4 0 +-3 0 +-2 0 +-1 0 diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.consensus.fq.gz b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.consensus.fq.gz new file mode 100644 index 00000000..33d87176 Binary files /dev/null and b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.consensus.fq.gz differ diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.pangraph.gfa b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.pangraph.gfa new file mode 100644 index 00000000..0e8ea678 --- /dev/null +++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.pangraph.gfa @@ -0,0 +1,3 @@ +H VN:Z:1.0 +S GC00006032 N FC:i:175 +S GC00010897 N FC:i:256 diff --git a/example/out_truth/pandora_discover_out/denovo_paths.txt b/example/out_truth/pandora_discover_out/denovo_paths.txt new file mode 100644 index 00000000..9d7821d6 --- /dev/null +++ b/example/out_truth/pandora_discover_out/denovo_paths.txt @@ -0,0 +1,34 @@ +2 samples +Sample toy_sample_1 +1 loci with denovo variants +GC00010897 +9 nodes +(0 [0, 110) ATGCAGATACGTGAACAGGGCCGCAAAATTCAGTGCATCCGCACCGTGTACGACAAGGCCATTGGCCGGGGTCGGCAGACGGTCATTGCCACACTGGCCCGCTATACGAC) +(2 [117, 118) G) +(3 [121, 171) GAAATGCCCACGACCGGGCTGGATGAGCTGACAGAGGCCGAACGCGAGAC) +(5 [178, 179) G) +(6 [182, 301) CTGGCCGAATGGCTGGCCAAGCGCCGGGAAGCCTCGCAGAAGTCGCAGGAGGCCTACACGGCCATGTCTGCGGATCGGTGGCTGGTCACGCTGGCCAAGGCCATCAGGGAAGGGCAGGA) +(8 [312, 316) ACTG) +(9 [319, 360) CGCCCCGAACAGGCGGCCGCGATCTGGCACGGCATGGGGGA) +(11 [369, 370) G) +(12 [374, 491) GTCGGCAAGGCCTTGCGCAAGGCTGGTCACGCGAAGCCCAAGGCGGTCAGAAAGGGCAAGCCGGTCGATCCGGCTGATCCCAAGGATCAAGGGGAGGGGGCACCAAAGGGGAAATGA) +2 denovo variants for this locus +44 C T +422 A T +Sample toy_sample_2 +1 loci with denovo variants +GC00006032 +11 nodes +(0 [0, 145) TTGAGTAAAACAATCCCCCGCGCTTATATAAGCGCGTTGATATTTTTAATTATTAACAAGCAACATCATGCTAATACAGACATACAAGGAGATCATCTCTCTTTGCCTGTTTTTTATTATTTCAGGAGTGTAAACACATTTTCCG) +(1 [148, 149) T) +(3 [156, 169) CTCCCTGGCTAAT) +(5 [176, 177) A) +(6 [180, 237) ACCACATTGGCATTTATGGAGCACATCACAATATTTCAATACCATTAAAGCACTGCA) +(8 [245, 246) T) +(9 [249, 267) CAAAATGAAACACTGCGA) +(11 [276, 277) T) +(12 [281, 290) ATTAAAATT) +(13 [294, 295) A) +(15 [304, 312) TTTCAATT) +1 denovo variants for this locus +49 A G diff --git a/example/out_truth/pandora_discover_out/toy_sample_1/denovo_paths.txt b/example/out_truth/pandora_discover_out/toy_sample_1/denovo_paths.txt new file mode 100644 index 00000000..991042b1 --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_1/denovo_paths.txt @@ -0,0 +1,16 @@ +Sample toy_sample_1 +1 loci with denovo variants +GC00010897 +9 nodes +(0 [0, 110) ATGCAGATACGTGAACAGGGCCGCAAAATTCAGTGCATCCGCACCGTGTACGACAAGGCCATTGGCCGGGGTCGGCAGACGGTCATTGCCACACTGGCCCGCTATACGAC) +(2 [117, 118) G) +(3 [121, 171) GAAATGCCCACGACCGGGCTGGATGAGCTGACAGAGGCCGAACGCGAGAC) +(5 [178, 179) G) +(6 [182, 301) CTGGCCGAATGGCTGGCCAAGCGCCGGGAAGCCTCGCAGAAGTCGCAGGAGGCCTACACGGCCATGTCTGCGGATCGGTGGCTGGTCACGCTGGCCAAGGCCATCAGGGAAGGGCAGGA) +(8 [312, 316) ACTG) +(9 [319, 360) CGCCCCGAACAGGCGGCCGCGATCTGGCACGGCATGGGGGA) +(11 [369, 370) G) +(12 [374, 491) GTCGGCAAGGCCTTGCGCAAGGCTGGTCACGCGAAGCCCAAGGCGGTCAGAAAGGGCAAGCCGGTCGATCCGGCTGATCCCAAGGATCAAGGGGAGGGGGCACCAAAGGGGAAATGA) +2 denovo variants for this locus +44 C T +422 A T diff --git a/example/out_truth/pandora_discover_out/toy_sample_1/pandora.consensus.fq.gz b/example/out_truth/pandora_discover_out/toy_sample_1/pandora.consensus.fq.gz new file mode 100644 index 00000000..3d6a43ca Binary files /dev/null and b/example/out_truth/pandora_discover_out/toy_sample_1/pandora.consensus.fq.gz differ diff --git a/example/out_truth/pandora_discover_out/toy_sample_1/pandora.pangraph.gfa b/example/out_truth/pandora_discover_out/toy_sample_1/pandora.pangraph.gfa new file mode 100644 index 00000000..843c6a0f --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_1/pandora.pangraph.gfa @@ -0,0 +1,3 @@ +H VN:Z:1.0 +S GC00006032 N FC:i:234 +S GC00010897 N FC:i:227 diff --git a/example/out_truth/pandora_discover_out/toy_sample_1/temp_child_00/candidate_regions_write_buffer.bin b/example/out_truth/pandora_discover_out/toy_sample_1/temp_child_00/candidate_regions_write_buffer.bin new file mode 100644 index 00000000..e723fefe --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_1/temp_child_00/candidate_regions_write_buffer.bin @@ -0,0 +1,10 @@ +22 serialization::archive 14 0 0 12 toy_sample_1 0 0 1 0 0 0 10 GC00010897 595 9 nodes +(0 [0, 110) ATGCAGATACGTGAACAGGGCCGCAAAATTCAGTGCATCCGCACCGTGTACGACAAGGCCATTGGCCGGGGTCGGCAGACGGTCATTGCCACACTGGCCCGCTATACGAC) +(2 [117, 118) G) +(3 [121, 171) GAAATGCCCACGACCGGGCTGGATGAGCTGACAGAGGCCGAACGCGAGAC) +(5 [178, 179) G) +(6 [182, 301) CTGGCCGAATGGCTGGCCAAGCGCCGGGAAGCCTCGCAGAAGTCGCAGGAGGCCTACACGGCCATGTCTGCGGATCGGTGGCTGGTCACGCTGGCCAAGGCCATCAGGGAAGGGCAGGA) +(8 [312, 316) ACTG) +(9 [319, 360) CGCCCCGAACAGGCGGCCGCGATCTGGCACGGCATGGGGGA) +(11 [369, 370) G) +(12 [374, 491) GTCGGCAAGGCCTTGCGCAAGGCTGGTCACGCGAAGCCCAAGGCGGTCAGAAAGGGCAAGCCGGTCGATCCGGCTGATCCCAAGGATCAAGGGGAGGGGGCACCAAAGGGGAAATGA) 0 0 1 0 0 0 10 GC00010897 0 0 2 0 6 44 C T 7 422 A T diff --git a/example/out_truth/pandora_discover_out/toy_sample_2/denovo_paths.txt b/example/out_truth/pandora_discover_out/toy_sample_2/denovo_paths.txt new file mode 100644 index 00000000..41297086 --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_2/denovo_paths.txt @@ -0,0 +1,17 @@ +Sample toy_sample_2 +1 loci with denovo variants +GC00006032 +11 nodes +(0 [0, 145) TTGAGTAAAACAATCCCCCGCGCTTATATAAGCGCGTTGATATTTTTAATTATTAACAAGCAACATCATGCTAATACAGACATACAAGGAGATCATCTCTCTTTGCCTGTTTTTTATTATTTCAGGAGTGTAAACACATTTTCCG) +(1 [148, 149) T) +(3 [156, 169) CTCCCTGGCTAAT) +(5 [176, 177) A) +(6 [180, 237) ACCACATTGGCATTTATGGAGCACATCACAATATTTCAATACCATTAAAGCACTGCA) +(8 [245, 246) T) +(9 [249, 267) CAAAATGAAACACTGCGA) +(11 [276, 277) T) +(12 [281, 290) ATTAAAATT) +(13 [294, 295) A) +(15 [304, 312) TTTCAATT) +1 denovo variants for this locus +49 A G diff --git a/example/out_truth/pandora_discover_out/toy_sample_2/pandora.consensus.fq.gz b/example/out_truth/pandora_discover_out/toy_sample_2/pandora.consensus.fq.gz new file mode 100644 index 00000000..17f747c4 Binary files /dev/null and b/example/out_truth/pandora_discover_out/toy_sample_2/pandora.consensus.fq.gz differ diff --git a/example/out_truth/pandora_discover_out/toy_sample_2/pandora.pangraph.gfa b/example/out_truth/pandora_discover_out/toy_sample_2/pandora.pangraph.gfa new file mode 100644 index 00000000..2ae02629 --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_2/pandora.pangraph.gfa @@ -0,0 +1,3 @@ +H VN:Z:1.0 +S GC00006032 N FC:i:111 +S GC00010897 N FC:i:256 diff --git a/example/out_truth/pandora_discover_out/toy_sample_2/temp_child_00/candidate_regions_write_buffer.bin b/example/out_truth/pandora_discover_out/toy_sample_2/temp_child_00/candidate_regions_write_buffer.bin new file mode 100644 index 00000000..82078ed1 --- /dev/null +++ b/example/out_truth/pandora_discover_out/toy_sample_2/temp_child_00/candidate_regions_write_buffer.bin @@ -0,0 +1,12 @@ +22 serialization::archive 14 0 0 12 toy_sample_2 0 0 1 0 0 0 10 GC00006032 441 11 nodes +(0 [0, 145) TTGAGTAAAACAATCCCCCGCGCTTATATAAGCGCGTTGATATTTTTAATTATTAACAAGCAACATCATGCTAATACAGACATACAAGGAGATCATCTCTCTTTGCCTGTTTTTTATTATTTCAGGAGTGTAAACACATTTTCCG) +(1 [148, 149) T) +(3 [156, 169) CTCCCTGGCTAAT) +(5 [176, 177) A) +(6 [180, 237) ACCACATTGGCATTTATGGAGCACATCACAATATTTCAATACCATTAAAGCACTGCA) +(8 [245, 246) T) +(9 [249, 267) CAAAATGAAACACTGCGA) +(11 [276, 277) T) +(12 [281, 290) ATTAAAATT) +(13 [294, 295) A) +(15 [304, 312) TTTCAATT) 0 0 1 0 0 0 10 GC00006032 0 0 1 0 6 49 A G diff --git a/example/out_truth/prgs/kmer_prgs/01/GC00006032.k15.w14.gfa b/example/out_truth/prgs/kmer_prgs/01/GC00006032.k15.w14.gfa new file mode 100644 index 00000000..65d27bd4 --- /dev/null +++ b/example/out_truth/prgs/kmer_prgs/01/GC00006032.k15.w14.gfa @@ -0,0 +1,97 @@ +H VN:Z:1.0 bn:Z:--linear --singlearr +S 0 1{[0, 0)} FC:i:0 RC:i:0 +L 0 + 1 + 0M +S 1 1{[9, 24)} FC:i:0 RC:i:0 +L 1 + 2 + 0M +S 2 1{[10, 25)} FC:i:0 RC:i:0 +L 2 + 3 + 0M +S 3 1{[15, 30)} FC:i:0 RC:i:0 +L 3 + 4 + 0M +S 4 1{[25, 40)} FC:i:0 RC:i:0 +L 4 + 5 + 0M +S 5 1{[29, 44)} FC:i:0 RC:i:0 +L 5 + 6 + 0M +S 6 1{[43, 58)} FC:i:0 RC:i:0 +L 6 + 7 + 0M +S 7 1{[52, 67)} FC:i:0 RC:i:0 +L 7 + 8 + 0M +S 8 1{[58, 73)} FC:i:0 RC:i:0 +L 8 + 9 + 0M +S 9 1{[61, 76)} FC:i:0 RC:i:0 +L 9 + 10 + 0M +S 10 1{[66, 81)} FC:i:0 RC:i:0 +L 10 + 11 + 0M +S 11 1{[67, 82)} FC:i:0 RC:i:0 +L 11 + 12 + 0M +S 12 1{[79, 94)} FC:i:0 RC:i:0 +L 12 + 13 + 0M +S 13 1{[82, 97)} FC:i:0 RC:i:0 +L 13 + 14 + 0M +S 14 1{[86, 101)} FC:i:0 RC:i:0 +L 14 + 15 + 0M +S 15 1{[93, 108)} FC:i:0 RC:i:0 +L 15 + 16 + 0M +S 16 1{[105, 120)} FC:i:0 RC:i:0 +L 16 + 17 + 0M +S 17 1{[115, 130)} FC:i:0 RC:i:0 +L 17 + 18 + 0M +S 18 1{[125, 140)} FC:i:0 RC:i:0 +L 18 + 19 + 0M +S 19 1{[129, 144)} FC:i:0 RC:i:0 +L 19 + 20 + 0M +L 19 + 21 + 0M +S 20 3{[133, 145)[148, 149)[156, 158)} FC:i:0 RC:i:0 +L 20 + 22 + 0M +L 20 + 23 + 0M +S 21 3{[137, 145)[152, 153)[156, 162)} FC:i:0 RC:i:0 +L 21 + 24 + 0M +S 22 3{[156, 169)[172, 173)[180, 181)} FC:i:0 RC:i:0 +L 22 + 25 + 0M +S 23 3{[138, 145)[148, 149)[156, 163)} FC:i:0 RC:i:0 +L 23 + 26 + 0M +S 24 3{[144, 145)[152, 153)[156, 169)} FC:i:0 RC:i:0 +L 24 + 25 + 0M +L 24 + 26 + 0M +S 25 3{[158, 169)[172, 173)[180, 183)} FC:i:0 RC:i:0 +L 25 + 27 + 0M +S 26 3{[161, 169)[176, 177)[180, 186)} FC:i:0 RC:i:0 +L 26 + 28 + 0M +S 27 3{[161, 169)[172, 173)[180, 186)} FC:i:0 RC:i:0 +L 27 + 29 + 0M +S 28 3{[166, 169)[176, 177)[180, 191)} FC:i:0 RC:i:0 +L 28 + 30 + 0M +S 29 2{[172, 173)[180, 194)} FC:i:0 RC:i:0 +L 29 + 30 + 0M +S 30 1{[186, 201)} FC:i:0 RC:i:0 +L 30 + 31 + 0M +S 31 1{[200, 215)} FC:i:0 RC:i:0 +L 31 + 32 + 0M +S 32 1{[214, 229)} FC:i:0 RC:i:0 +L 32 + 33 + 0M +S 33 1{[218, 233)} FC:i:0 RC:i:0 +L 33 + 34 + 0M +L 33 + 35 + 0M +S 34 3{[229, 237)[245, 246)[249, 255)} FC:i:0 RC:i:0 +L 34 + 36 + 0M +S 35 1{[222, 237)} FC:i:0 RC:i:0 +L 35 + 37 + 0M +S 36 3{[230, 237)[245, 246)[249, 256)} FC:i:0 RC:i:0 +L 36 + 38 + 0M +S 37 3{[229, 237)[240, 241)[249, 255)} FC:i:0 RC:i:0 +L 37 + 39 + 0M +S 38 3{[236, 237)[245, 246)[249, 262)} FC:i:0 RC:i:0 +L 38 + 40 + 0M +L 38 + 41 + 0M +S 39 1{[250, 265)} FC:i:0 RC:i:0 +L 39 + 42 + 0M +L 39 + 41 + 0M +S 40 3{[259, 267)[271, 272)[281, 287)} FC:i:0 RC:i:0 +L 40 + 44 + 0M +S 41 3{[259, 267)[276, 277)[281, 287)} FC:i:0 RC:i:0 +L 41 + 43 + 0M +L 41 + 44 + 0M +S 42 2{[253, 267)[271, 272)} FC:i:0 RC:i:0 +L 42 + 40 + 0M +S 43 5{[264, 267)[276, 277)[281, 290)[294, 295)[304, 305)} FC:i:0 RC:i:0 +L 43 + 44 + 0M +S 44 1{[312, 312)} FC:i:0 RC:i:0 diff --git a/example/out_truth/prgs/kmer_prgs/01/GC00010897.k15.w14.gfa b/example/out_truth/prgs/kmer_prgs/01/GC00010897.k15.w14.gfa new file mode 100644 index 00000000..cb572d40 --- /dev/null +++ b/example/out_truth/prgs/kmer_prgs/01/GC00010897.k15.w14.gfa @@ -0,0 +1,146 @@ +H VN:Z:1.0 bn:Z:--linear --singlearr +S 0 1{[0, 0)} FC:i:0 RC:i:0 +L 0 + 1 + 0M +S 1 1{[6, 21)} FC:i:0 RC:i:0 +L 1 + 2 + 0M +S 2 1{[13, 28)} FC:i:0 RC:i:0 +L 2 + 3 + 0M +S 3 1{[24, 39)} FC:i:0 RC:i:0 +L 3 + 4 + 0M +S 4 1{[25, 40)} FC:i:0 RC:i:0 +L 4 + 5 + 0M +S 5 1{[29, 44)} FC:i:0 RC:i:0 +L 5 + 6 + 0M +S 6 1{[42, 57)} FC:i:0 RC:i:0 +L 6 + 7 + 0M +S 7 1{[49, 64)} FC:i:0 RC:i:0 +L 7 + 8 + 0M +S 8 1{[51, 66)} FC:i:0 RC:i:0 +L 8 + 9 + 0M +S 9 1{[52, 67)} FC:i:0 RC:i:0 +L 9 + 10 + 0M +S 10 1{[57, 72)} FC:i:0 RC:i:0 +L 10 + 11 + 0M +S 11 1{[68, 83)} FC:i:0 RC:i:0 +L 11 + 12 + 0M +S 12 1{[75, 90)} FC:i:0 RC:i:0 +L 12 + 13 + 0M +S 13 1{[76, 91)} FC:i:0 RC:i:0 +L 13 + 14 + 0M +S 14 1{[78, 93)} FC:i:0 RC:i:0 +L 14 + 15 + 0M +S 15 1{[88, 103)} FC:i:0 RC:i:0 +L 15 + 16 + 0M +S 16 1{[89, 104)} FC:i:0 RC:i:0 +L 16 + 17 + 0M +L 16 + 18 + 0M +S 17 3{[103, 110)[113, 114)[121, 128)} FC:i:0 RC:i:0 +L 17 + 19 + 0M +S 18 3{[99, 110)[117, 118)[121, 124)} FC:i:0 RC:i:0 +L 18 + 20 + 0M +S 19 1{[127, 142)} FC:i:0 RC:i:0 +L 19 + 21 + 0M +S 20 3{[107, 110)[117, 118)[121, 132)} FC:i:0 RC:i:0 +L 20 + 21 + 0M +S 21 1{[130, 145)} FC:i:0 RC:i:0 +L 21 + 22 + 0M +S 22 1{[132, 147)} FC:i:0 RC:i:0 +L 22 + 23 + 0M +S 23 1{[143, 158)} FC:i:0 RC:i:0 +L 23 + 24 + 0M +S 24 1{[147, 162)} FC:i:0 RC:i:0 +L 24 + 25 + 0M +S 25 1{[150, 165)} FC:i:0 RC:i:0 +L 25 + 26 + 0M +L 25 + 27 + 0M +S 26 3{[159, 171)[174, 175)[182, 184)} FC:i:0 RC:i:0 +L 26 + 28 + 0M +S 27 3{[163, 171)[178, 179)[182, 188)} FC:i:0 RC:i:0 +L 27 + 29 + 0M +S 28 3{[162, 171)[174, 175)[182, 187)} FC:i:0 RC:i:0 +L 28 + 29 + 0M +S 29 1{[184, 199)} FC:i:0 RC:i:0 +L 29 + 30 + 0M +S 30 1{[195, 210)} FC:i:0 RC:i:0 +L 30 + 31 + 0M +S 31 1{[209, 224)} FC:i:0 RC:i:0 +L 31 + 32 + 0M +S 32 1{[220, 235)} FC:i:0 RC:i:0 +L 32 + 33 + 0M +S 33 1{[224, 239)} FC:i:0 RC:i:0 +L 33 + 34 + 0M +S 34 1{[228, 243)} FC:i:0 RC:i:0 +L 34 + 35 + 0M +S 35 1{[239, 254)} FC:i:0 RC:i:0 +L 35 + 36 + 0M +S 36 1{[251, 266)} FC:i:0 RC:i:0 +L 36 + 37 + 0M +S 37 1{[261, 276)} FC:i:0 RC:i:0 +L 37 + 38 + 0M +S 38 1{[262, 277)} FC:i:0 RC:i:0 +L 38 + 39 + 0M +S 39 1{[263, 278)} FC:i:0 RC:i:0 +L 39 + 40 + 0M +S 40 1{[271, 286)} FC:i:0 RC:i:0 +L 40 + 41 + 0M +S 41 1{[273, 288)} FC:i:0 RC:i:0 +L 41 + 42 + 0M +S 42 1{[275, 290)} FC:i:0 RC:i:0 +L 42 + 43 + 0M +S 43 1{[281, 296)} FC:i:0 RC:i:0 +L 43 + 44 + 0M +L 43 + 45 + 0M +S 44 3{[292, 301)[312, 316)[319, 321)} FC:i:0 RC:i:0 +L 44 + 46 + 0M +S 45 3{[293, 301)[304, 308)[319, 322)} FC:i:0 RC:i:0 +L 45 + 47 + 0M +S 46 3{[293, 301)[312, 316)[319, 322)} FC:i:0 RC:i:0 +L 46 + 48 + 0M +S 47 2{[307, 308)[319, 333)} FC:i:0 RC:i:0 +L 47 + 49 + 0M +S 48 2{[313, 316)[319, 331)} FC:i:0 RC:i:0 +L 48 + 49 + 0M +S 49 1{[322, 337)} FC:i:0 RC:i:0 +L 49 + 50 + 0M +S 50 1{[336, 351)} FC:i:0 RC:i:0 +L 50 + 51 + 0M +S 51 1{[343, 358)} FC:i:0 RC:i:0 +L 51 + 52 + 0M +L 51 + 53 + 0M +S 52 3{[357, 360)[364, 365)[374, 385)} FC:i:0 RC:i:0 +L 52 + 54 + 0M +S 53 3{[347, 360)[369, 370)[374, 375)} FC:i:0 RC:i:0 +L 53 + 55 + 0M +S 54 1{[376, 391)} FC:i:0 RC:i:0 +L 54 + 56 + 0M +S 55 3{[353, 360)[369, 370)[374, 381)} FC:i:0 RC:i:0 +L 55 + 54 + 0M +S 56 1{[379, 394)} FC:i:0 RC:i:0 +L 56 + 57 + 0M +S 57 1{[391, 406)} FC:i:0 RC:i:0 +L 57 + 58 + 0M +S 58 1{[399, 414)} FC:i:0 RC:i:0 +L 58 + 59 + 0M +S 59 1{[407, 422)} FC:i:0 RC:i:0 +L 59 + 60 + 0M +S 60 1{[410, 425)} FC:i:0 RC:i:0 +L 60 + 61 + 0M +S 61 1{[415, 430)} FC:i:0 RC:i:0 +L 61 + 62 + 0M +S 62 1{[426, 441)} FC:i:0 RC:i:0 +L 62 + 63 + 0M +S 63 1{[433, 448)} FC:i:0 RC:i:0 +L 63 + 64 + 0M +S 64 1{[434, 449)} FC:i:0 RC:i:0 +L 64 + 65 + 0M +S 65 1{[440, 455)} FC:i:0 RC:i:0 +L 65 + 66 + 0M +S 66 1{[452, 467)} FC:i:0 RC:i:0 +L 66 + 67 + 0M +S 67 1{[465, 480)} FC:i:0 RC:i:0 +L 67 + 68 + 0M +S 68 1{[472, 487)} FC:i:0 RC:i:0 +L 68 + 69 + 0M +S 69 1{[476, 491)} FC:i:0 RC:i:0 +L 69 + 70 + 0M +S 70 1{[491, 491)} FC:i:0 RC:i:0 diff --git a/example/out_truth/prgs/pangenome.prg.fa.k15.w14.idx b/example/out_truth/prgs/pangenome.prg.fa.k15.w14.idx new file mode 100644 index 00000000..e0f63f71 --- /dev/null +++ b/example/out_truth/prgs/pangenome.prg.fa.k15.w14.idx @@ -0,0 +1,113 @@ +112 +16318469 1 (1, 5{[264, 267)[276, 277)[281, 290)[294, 295)[304, 305)}, 43, 1) +95908974 1 (1, 2{[253, 267)[271, 272)}, 42, 0) +74944522 1 (1, 3{[259, 267)[276, 277)[281, 287)}, 41, 0) +25603268 1 (1, 3{[259, 267)[271, 272)[281, 287)}, 40, 1) +150075561 1 (1, 1{[250, 265)}, 39, 1) +92543452 1 (1, 3{[236, 237)[245, 246)[249, 262)}, 38, 1) +182535811 1 (1, 3{[229, 237)[240, 241)[249, 255)}, 37, 1) +22204066 1 (1, 3{[230, 237)[245, 246)[249, 256)}, 36, 0) +136923223 1 (1, 3{[229, 237)[245, 246)[249, 255)}, 34, 1) +150896025 1 (1, 1{[218, 233)}, 33, 1) +50450125 1 (1, 1{[214, 229)}, 32, 1) +76253524 1 (1, 1{[200, 215)}, 31, 0) +61544635 1 (1, 1{[186, 201)}, 30, 0) +32095090 1 (1, 2{[172, 173)[180, 194)}, 29, 1) +84155375 1 (1, 3{[166, 169)[176, 177)[180, 191)}, 28, 0) +964725 1 (1, 3{[161, 169)[172, 173)[180, 186)}, 27, 1) +22900170 1 (1, 3{[161, 169)[176, 177)[180, 186)}, 26, 1) +58898711 1 (1, 3{[158, 169)[172, 173)[180, 183)}, 25, 1) +62158241 1 (1, 3{[144, 145)[152, 153)[156, 169)}, 24, 1) +182808637 1 (1, 3{[138, 145)[148, 149)[156, 163)}, 23, 1) +126788003 1 (1, 3{[156, 169)[172, 173)[180, 181)}, 22, 0) +70667501 1 (1, 3{[137, 145)[152, 153)[156, 162)}, 21, 0) +80230343 1 (1, 3{[133, 145)[148, 149)[156, 158)}, 20, 0) +40017473 1 (1, 1{[129, 144)}, 19, 1) +10144007 1 (1, 1{[125, 140)}, 18, 0) +87464180 1 (1, 1{[115, 130)}, 17, 0) +45109196 1 (1, 1{[93, 108)}, 15, 1) +62100866 1 (1, 1{[86, 101)}, 14, 1) +84500547 1 (1, 1{[82, 97)}, 13, 0) +117300766 1 (1, 1{[79, 94)}, 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b/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00010897.fa.pickle new file mode 100644 index 00000000..818594bf Binary files /dev/null and b/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00010897.fa.pickle differ diff --git a/example/out_truth/updated_prgs/kmer_prgs/01/GC00006032.k15.w14.gfa b/example/out_truth/updated_prgs/kmer_prgs/01/GC00006032.k15.w14.gfa new file mode 100644 index 00000000..92203181 --- /dev/null +++ b/example/out_truth/updated_prgs/kmer_prgs/01/GC00006032.k15.w14.gfa @@ -0,0 +1,102 @@ +H VN:Z:1.0 bn:Z:--linear --singlearr +S 0 1{[0, 0)} FC:i:0 RC:i:0 +L 0 + 1 + 0M +S 1 1{[9, 24)} FC:i:0 RC:i:0 +L 1 + 2 + 0M +S 2 1{[10, 25)} FC:i:0 RC:i:0 +L 2 + 3 + 0M +S 3 1{[15, 30)} FC:i:0 RC:i:0 +L 3 + 4 + 0M +S 4 1{[25, 40)} FC:i:0 RC:i:0 +L 4 + 5 + 0M +S 5 1{[29, 44)} FC:i:0 RC:i:0 +L 5 + 6 + 0M +L 5 + 7 + 0M +S 6 3{[43, 48)[51, 52)[59, 68)} FC:i:0 RC:i:0 +L 6 + 8 + 0M +S 7 3{[43, 48)[55, 56)[59, 68)} FC:i:0 RC:i:0 +L 7 + 9 + 0M +S 8 1{[62, 77)} FC:i:0 RC:i:0 +L 8 + 10 + 0M +S 9 3{[45, 48)[55, 56)[59, 70)} FC:i:0 RC:i:0 +L 9 + 10 + 0M +S 10 1{[68, 83)} FC:i:0 RC:i:0 +L 10 + 11 + 0M +S 11 1{[71, 86)} FC:i:0 RC:i:0 +L 11 + 12 + 0M +S 12 1{[76, 91)} FC:i:0 RC:i:0 +L 12 + 13 + 0M +S 13 1{[77, 92)} FC:i:0 RC:i:0 +L 13 + 14 + 0M +S 14 1{[89, 104)} FC:i:0 RC:i:0 +L 14 + 15 + 0M +S 15 1{[92, 107)} FC:i:0 RC:i:0 +L 15 + 16 + 0M +S 16 1{[96, 111)} FC:i:0 RC:i:0 +L 16 + 17 + 0M +S 17 1{[103, 118)} FC:i:0 RC:i:0 +L 17 + 18 + 0M +S 18 1{[115, 130)} FC:i:0 RC:i:0 +L 18 + 19 + 0M +S 19 1{[125, 140)} FC:i:0 RC:i:0 +L 19 + 20 + 0M +S 20 1{[135, 150)} FC:i:0 RC:i:0 +L 20 + 21 + 0M +S 21 1{[139, 154)} FC:i:0 RC:i:0 +L 21 + 22 + 0M +L 21 + 23 + 0M +S 22 3{[143, 155)[158, 159)[166, 168)} FC:i:0 RC:i:0 +L 22 + 24 + 0M +L 22 + 25 + 0M +S 23 3{[147, 155)[162, 163)[166, 172)} FC:i:0 RC:i:0 +L 23 + 26 + 0M +S 24 3{[166, 179)[182, 183)[191, 192)} FC:i:0 RC:i:0 +L 24 + 27 + 0M +S 25 3{[148, 155)[158, 159)[166, 173)} FC:i:0 RC:i:0 +L 25 + 28 + 0M +S 26 3{[154, 155)[162, 163)[166, 179)} FC:i:0 RC:i:0 +L 26 + 27 + 0M +L 26 + 28 + 0M +S 27 3{[168, 179)[182, 183)[191, 194)} FC:i:0 RC:i:0 +L 27 + 29 + 0M +S 28 3{[171, 179)[187, 188)[191, 197)} FC:i:0 RC:i:0 +L 28 + 30 + 0M +S 29 3{[171, 179)[182, 183)[191, 197)} FC:i:0 RC:i:0 +L 29 + 31 + 0M +S 30 3{[176, 179)[187, 188)[191, 202)} FC:i:0 RC:i:0 +L 30 + 32 + 0M +S 31 2{[182, 183)[191, 205)} FC:i:0 RC:i:0 +L 31 + 32 + 0M +S 32 1{[197, 212)} FC:i:0 RC:i:0 +L 32 + 33 + 0M +S 33 1{[211, 226)} FC:i:0 RC:i:0 +L 33 + 34 + 0M +S 34 1{[225, 240)} FC:i:0 RC:i:0 +L 34 + 35 + 0M +S 35 1{[229, 244)} FC:i:0 RC:i:0 +L 35 + 36 + 0M +L 35 + 37 + 0M +S 36 3{[240, 248)[257, 258)[262, 268)} FC:i:0 RC:i:0 +L 36 + 38 + 0M +S 37 1{[233, 248)} FC:i:0 RC:i:0 +L 37 + 39 + 0M +S 38 3{[241, 248)[257, 258)[262, 269)} FC:i:0 RC:i:0 +L 38 + 40 + 0M +S 39 3{[240, 248)[252, 253)[262, 268)} FC:i:0 RC:i:0 +L 39 + 41 + 0M +S 40 3{[247, 248)[257, 258)[262, 275)} FC:i:0 RC:i:0 +L 40 + 42 + 0M +L 40 + 43 + 0M +S 41 1{[263, 278)} FC:i:0 RC:i:0 +L 41 + 44 + 0M +L 41 + 43 + 0M +S 42 3{[272, 280)[284, 285)[294, 300)} FC:i:0 RC:i:0 +L 42 + 46 + 0M +S 43 3{[272, 280)[289, 290)[294, 300)} FC:i:0 RC:i:0 +L 43 + 45 + 0M +L 43 + 46 + 0M +S 44 2{[266, 280)[284, 285)} FC:i:0 RC:i:0 +L 44 + 42 + 0M +S 45 5{[277, 280)[289, 290)[294, 303)[307, 308)[317, 318)} FC:i:0 RC:i:0 +L 45 + 46 + 0M +S 46 1{[325, 325)} FC:i:0 RC:i:0 diff --git a/example/out_truth/updated_prgs/kmer_prgs/01/GC00010897.k15.w14.gfa b/example/out_truth/updated_prgs/kmer_prgs/01/GC00010897.k15.w14.gfa new file mode 100644 index 00000000..5e19cfdb --- /dev/null +++ b/example/out_truth/updated_prgs/kmer_prgs/01/GC00010897.k15.w14.gfa @@ -0,0 +1,158 @@ +H VN:Z:1.0 bn:Z:--linear --singlearr +S 0 1{[0, 0)} FC:i:0 RC:i:0 +L 0 + 1 + 0M +S 1 1{[6, 21)} FC:i:0 RC:i:0 +L 1 + 2 + 0M +S 2 1{[13, 28)} FC:i:0 RC:i:0 +L 2 + 3 + 0M +S 3 1{[24, 39)} FC:i:0 RC:i:0 +L 3 + 4 + 0M +S 4 1{[25, 40)} FC:i:0 RC:i:0 +L 4 + 5 + 0M +L 4 + 6 + 0M +S 5 2{[29, 43)[46, 47)} FC:i:0 RC:i:0 +L 5 + 7 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1{[140, 155)} FC:i:0 RC:i:0 +L 24 + 25 + 0M +S 25 1{[142, 157)} FC:i:0 RC:i:0 +L 25 + 26 + 0M +S 26 1{[153, 168)} FC:i:0 RC:i:0 +L 26 + 27 + 0M +S 27 1{[157, 172)} FC:i:0 RC:i:0 +L 27 + 28 + 0M +S 28 1{[160, 175)} FC:i:0 RC:i:0 +L 28 + 29 + 0M +L 28 + 30 + 0M +S 29 3{[169, 181)[184, 185)[193, 195)} FC:i:0 RC:i:0 +L 29 + 31 + 0M +S 30 3{[173, 181)[189, 190)[193, 199)} FC:i:0 RC:i:0 +L 30 + 32 + 0M +S 31 3{[172, 181)[184, 185)[193, 198)} FC:i:0 RC:i:0 +L 31 + 32 + 0M +S 32 1{[195, 210)} FC:i:0 RC:i:0 +L 32 + 33 + 0M +S 33 1{[206, 221)} FC:i:0 RC:i:0 +L 33 + 34 + 0M +S 34 1{[220, 235)} FC:i:0 RC:i:0 +L 34 + 35 + 0M +S 35 1{[231, 246)} FC:i:0 RC:i:0 +L 35 + 36 + 0M +S 36 1{[235, 250)} FC:i:0 RC:i:0 +L 36 + 37 + 0M +S 37 1{[239, 254)} FC:i:0 RC:i:0 +L 37 + 38 + 0M +S 38 1{[250, 265)} FC:i:0 RC:i:0 +L 38 + 39 + 0M +S 39 1{[262, 277)} FC:i:0 RC:i:0 +L 39 + 40 + 0M +S 40 1{[272, 287)} FC:i:0 RC:i:0 +L 40 + 41 + 0M +S 41 1{[273, 288)} FC:i:0 RC:i:0 +L 41 + 42 + 0M +S 42 1{[274, 289)} FC:i:0 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1{[392, 407)} FC:i:0 RC:i:0 +L 59 + 60 + 0M +S 60 1{[404, 419)} FC:i:0 RC:i:0 +L 60 + 61 + 0M +S 61 1{[412, 427)} FC:i:0 RC:i:0 +L 61 + 62 + 0M +S 62 1{[420, 435)} FC:i:0 RC:i:0 +L 62 + 63 + 0M +S 63 1{[423, 438)} FC:i:0 RC:i:0 +L 63 + 64 + 0M +S 64 1{[428, 443)} FC:i:0 RC:i:0 +L 64 + 65 + 0M +S 65 1{[439, 454)} FC:i:0 RC:i:0 +L 65 + 66 + 0M +S 66 1{[446, 461)} FC:i:0 RC:i:0 +L 66 + 67 + 0M +S 67 1{[447, 462)} FC:i:0 RC:i:0 +L 67 + 68 + 0M +S 68 1{[453, 468)} FC:i:0 RC:i:0 +L 68 + 69 + 0M +S 69 1{[465, 480)} FC:i:0 RC:i:0 +L 69 + 70 + 0M +L 69 + 71 + 0M +S 70 3{[468, 481)[490, 491)[495, 496)} FC:i:0 RC:i:0 +L 70 + 72 + 0M +S 71 3{[478, 481)[485, 486)[495, 506)} FC:i:0 RC:i:0 +L 71 + 73 + 0M +S 72 3{[476, 481)[490, 491)[495, 504)} FC:i:0 RC:i:0 +L 72 + 73 + 0M +S 73 1{[498, 513)} FC:i:0 RC:i:0 +L 73 + 74 + 0M +S 74 1{[502, 517)} FC:i:0 RC:i:0 +L 74 + 75 + 0M +S 75 1{[517, 517)} FC:i:0 RC:i:0 diff --git a/example/out_truth/updated_prgs/pangenome_updated.prg.fa.k15.w14.idx b/example/out_truth/updated_prgs/pangenome_updated.prg.fa.k15.w14.idx new file mode 100644 index 00000000..8f408f12 --- /dev/null +++ b/example/out_truth/updated_prgs/pangenome_updated.prg.fa.k15.w14.idx @@ -0,0 +1,120 @@ +119 +16318469 1 (1, 5{[277, 280)[289, 290)[294, 303)[307, 308)[317, 318)}, 45, 1) +95908974 1 (1, 2{[266, 280)[284, 285)}, 44, 0) +74944522 1 (1, 3{[272, 280)[289, 290)[294, 300)}, 43, 0) +25603268 1 (1, 3{[272, 280)[284, 285)[294, 300)}, 42, 1) +150075561 1 (1, 1{[263, 278)}, 41, 1) +92543452 1 (1, 3{[247, 248)[257, 258)[262, 275)}, 40, 1) +182535811 1 (1, 3{[240, 248)[252, 253)[262, 268)}, 39, 1) +22204066 1 (1, 3{[241, 248)[257, 258)[262, 269)}, 38, 0) +158006043 1 (1, 1{[233, 248)}, 37, 1) +136923223 1 (1, 3{[240, 248)[257, 258)[262, 268)}, 36, 1) +150896025 1 (1, 1{[229, 244)}, 35, 1) +50450125 1 (1, 1{[225, 240)}, 34, 1) +76253524 1 (1, 1{[211, 226)}, 33, 0) +61544635 1 (1, 1{[197, 212)}, 32, 0) +32095090 1 (1, 2{[182, 183)[191, 205)}, 31, 1) +84155375 1 (1, 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+118310049 1 (1, 1{[62, 77)}, 8, 1) +23944745 1 (1, 3{[43, 48)[55, 56)[59, 68)}, 7, 0) +12634334 1 (1, 3{[43, 48)[51, 52)[59, 68)}, 6, 0) +32446550 1 (1, 1{[29, 44)}, 5, 1) +85119856 1 (1, 1{[25, 40)}, 4, 1) +146396092 1 (1, 1{[15, 30)}, 3, 0) +117410367 1 (1, 1{[10, 25)}, 2, 0) +47412201 1 (1, 1{[9, 24)}, 1, 0) +454860 1 (0, 1{[502, 517)}, 74, 1) +10470925 1 (0, 1{[498, 513)}, 73, 0) +121176941 1 (0, 3{[476, 481)[490, 491)[495, 504)}, 72, 1) +16393675 1 (0, 3{[478, 481)[485, 486)[495, 506)}, 71, 1) +13727052 1 (0, 3{[468, 481)[490, 491)[495, 496)}, 70, 0) +24884945 1 (0, 1{[465, 480)}, 69, 1) +39358686 1 (0, 1{[453, 468)}, 68, 1) +35934452 1 (0, 1{[447, 462)}, 67, 0) +194061 1 (0, 1{[446, 461)}, 66, 0) +3212702 1 (0, 1{[439, 454)}, 65, 0) +36203250 1 (0, 1{[428, 443)}, 64, 0) +85606590 1 (0, 1{[423, 438)}, 63, 0) +109416972 1 (0, 1{[420, 435)}, 62, 0) +142092369 1 (0, 1{[412, 427)}, 61, 0) +27165023 1 (0, 1{[404, 419)}, 60, 1) +33357868 1 (0, 1{[392, 407)}, 59, 1) +1276048 1 (0, 1{[389, 404)}, 57, 1) +71473097 1 (0, 3{[360, 373)[382, 383)[387, 388)}, 56, 1) +8869878 1 (0, 3{[370, 373)[377, 378)[387, 398)}, 55, 1) +403679 1 (0, 1{[356, 371)}, 54, 1) +73010802 1 (0, 1{[349, 364)}, 53, 1) +21552618 1 (0, 1{[335, 350)}, 52, 1) +20504340 1 (0, 2{[325, 328)[332, 344)}, 51, 0) +140531031 1 (0, 2{[319, 320)[332, 346)}, 50, 0) +24327029 1 (0, 3{[304, 312)[324, 328)[332, 335)}, 49, 0) +10770263 1 (0, 3{[304, 312)[316, 320)[332, 335)}, 48, 1) +116049953 1 (0, 3{[303, 312)[324, 328)[332, 334)}, 47, 1) +124991398 1 (0, 1{[292, 307)}, 46, 0) +46739838 1 (0, 1{[286, 301)}, 45, 1) +24932839 1 (0, 1{[284, 299)}, 44, 1) +5793861 1 (0, 1{[282, 297)}, 43, 0) +40417193 1 (0, 1{[274, 289)}, 42, 1) +47369520 1 (0, 1{[272, 287)}, 40, 1) +57951963 1 (0, 1{[262, 277)}, 39, 0) +82000267 1 (0, 3{[366, 373)[382, 383)[387, 394)}, 58, 0) +105221040 1 (0, 1{[250, 265)}, 38, 1) +18585087 1 (0, 1{[239, 254)}, 37, 0) +58759004 1 (0, 1{[235, 250)}, 36, 1) +46243831 1 (0, 1{[273, 288)}, 41, 1) +158709222 1 (0, 1{[231, 246)}, 35, 0) +70513877 1 (0, 1{[220, 235)}, 34, 1) +69201700 1 (0, 1{[206, 221)}, 33, 0) +13740578 1 (0, 1{[195, 210)}, 32, 1) +34839656 1 (0, 3{[172, 181)[184, 185)[193, 198)}, 31, 0) +38692934 1 (0, 3{[173, 181)[189, 190)[193, 199)}, 30, 0) +32296303 1 (0, 3{[169, 181)[184, 185)[193, 195)}, 29, 0) +14936588 1 (0, 1{[160, 175)}, 28, 1) +27686752 1 (0, 1{[157, 172)}, 27, 0) +96552299 1 (0, 1{[153, 168)}, 26, 0) +55824476 1 (0, 1{[142, 157)}, 25, 1) +37634093 1 (0, 1{[140, 155)}, 24, 0) +27254804 1 (0, 3{[117, 120)[127, 128)[131, 142)}, 23, 1) +39280491 1 (0, 1{[137, 152)}, 22, 1) +135073096 1 (0, 3{[109, 120)[127, 128)[131, 134)}, 21, 0) +91569063 1 (0, 1{[99, 114)}, 19, 0) +31238650 1 (0, 3{[113, 120)[123, 124)[131, 138)}, 20, 1) +84550898 1 (0, 1{[98, 113)}, 18, 0) +83969001 1 (0, 1{[88, 103)}, 17, 0) +62421088 1 (0, 1{[86, 101)}, 16, 1) +92281898 1 (0, 1{[85, 100)}, 15, 0) +138968336 1 (0, 1{[78, 93)}, 14, 0) +72337557 1 (0, 1{[67, 82)}, 13, 0) +68189800 1 (0, 1{[62, 77)}, 12, 1) +52616670 1 (0, 1{[61, 76)}, 11, 1) +117600578 1 (0, 1{[55, 70)}, 10, 0) +15850244 1 (0, 1{[59, 74)}, 9, 1) +182852002 1 (0, 3{[41, 43)[50, 51)[54, 66)}, 8, 1) +52061784 1 (0, 3{[42, 43)[46, 47)[54, 67)}, 7, 1) +42564047 1 (0, 3{[30, 43)[50, 51)[54, 55)}, 6, 1) +58311598 1 (0, 2{[29, 43)[46, 47)}, 5, 1) +31358832 1 (0, 1{[25, 40)}, 4, 0) +154624683 1 (0, 1{[24, 39)}, 3, 1) +173965435 1 (0, 1{[13, 28)}, 2, 1) +84235074 1 (0, 1{[6, 21)}, 1, 1) diff --git a/example/run_pandora.sh b/example/run_pandora.sh index b765c577..e2d1284e 100755 --- a/example/run_pandora.sh +++ b/example/run_pandora.sh @@ -1,12 +1,14 @@ #!/usr/bin/env bash set -eu -# configs -pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0" -pandora_executable="./pandora-linux-precompiled-v0.9.0" -make_prg_URL="https://github.com/leoisl/make_prg/releases/download/v0.2.0/make_prg_0.2.0" -make_prg_executable="./make_prg_0.2.0" - +######################################################################################################################## +# argument parsing +if [[ "$#" -gt 1 || ( "$#" -eq 1 && "$1" != "conda" ) ]] ; then + echo "Illegal parameters." + echo "Usage: $0 or $0 conda" + exit 1 +fi +######################################################################################################################## function download_tool { URL=$1 @@ -15,25 +17,43 @@ function download_tool { chmod +x "${executable}" } -download_tool "${pandora_URL}" "${pandora_executable}" +# setup tools +if [ "$#" -eq 0 ] ; then + # not conda env + pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.1/pandora-linux-precompiled-v0.9.1" + pandora_executable="./pandora-linux-precompiled-v0.9.1" + download_tool "${pandora_URL}" "${pandora_executable}" +else + # conda env + pandora_executable="pandora" +fi + +make_prg_URL="https://github.com/leoisl/make_prg/releases/download/v0.2.0/make_prg_0.2.0" +make_prg_executable="./make_prg_0.2.0" download_tool "${make_prg_URL}" "${make_prg_executable}" echo "Running pandora without denovo..." echo "Running ${make_prg_executable} from_msa" -"${make_prg_executable}" from_msa --input msas/ --output_prefix prgs/pangenome +"${make_prg_executable}" from_msa --threads 1 --input msas/ --output_prefix out/prgs/pangenome echo "Running ${pandora_executable} index" -"${pandora_executable}" index prgs/pangenome.prg.fa +"${pandora_executable}" index --threads 1 out/prgs/pangenome.prg.fa echo "Running ${pandora_executable} compare" -"${pandora_executable}" compare --genotype -o output_toy_example_no_denovo prgs/pangenome.prg.fa reads/read_index.tsv +"${pandora_executable}" compare --threads 1 --genotype -o out/output_toy_example_no_denovo out/prgs/pangenome.prg.fa reads/read_index.tsv echo "Running pandora without denovo - done!" echo "Running pandora with denovo..." echo "Running ${pandora_executable} discover" -"${pandora_executable}" discover --outdir pandora_discover_out prgs/pangenome.prg.fa reads/read_index.tsv +"${pandora_executable}" discover --threads 1 --outdir out/pandora_discover_out out/prgs/pangenome.prg.fa reads/read_index.tsv echo "Running ${make_prg_executable} update" -"${make_prg_executable}" update --update_DS prgs/pangenome.update_DS --denovo_paths pandora_discover_out/denovo_paths.txt --output_prefix updated_prgs/pangenome_updated +"${make_prg_executable}" update --threads 1 --update_DS out/prgs/pangenome.update_DS --denovo_paths out/pandora_discover_out/denovo_paths.txt --output_prefix out/updated_prgs/pangenome_updated echo "Running ${pandora_executable} index on updated PRGs" -"${pandora_executable}" index updated_prgs/pangenome_updated.prg.fa +"${pandora_executable}" index --threads 1 out/updated_prgs/pangenome_updated.prg.fa echo "Running ${pandora_executable} compare" -"${pandora_executable}" compare --genotype -o output_toy_example_with_denovo updated_prgs/pangenome_updated.prg.fa reads/read_index.tsv +"${pandora_executable}" compare --threads 1 --genotype -o out/output_toy_example_with_denovo out/updated_prgs/pangenome_updated.prg.fa reads/read_index.tsv echo "Running pandora with denovo - done!" + +if diff -rq -I '##fileDate.*' out out_truth ; then + echo "Example run produced the expected result" +else + echo "ERROR: Example run DID NOT produce the expected result" +fi diff --git a/scripts/create_archives.sh b/scripts/create_archives.sh new file mode 100755 index 00000000..3991dea0 --- /dev/null +++ b/scripts/create_archives.sh @@ -0,0 +1,54 @@ +#!/bin/bash +# run from project root: scripts/create_archives.sh +# based on https://github.com/nzanepro/git-archive-submodules/blob/master/bin/git-archive-submodules.sh +set -eu + +######################################################################################################################## +# argument parsing +if [ "$#" -ne 1 ]; then + echo "Illegal number of parameters." + echo "Usage: $0 " + echo "Example: $0 0.8.0" + exit 1 +fi +PANDORA_VERSION="$1" +######################################################################################################################## + +######################################################################################################################## +# configs +PANDORA_URL="https://github.com/rmcolq/pandora" +ARCHIVES_DIR="./archives" +######################################################################################################################## + +######################################################################################################################## +# main script +ARCHIVES_DIR=$(realpath "${ARCHIVES_DIR}") +if [ -d "${ARCHIVES_DIR}" ]; then + echo "Please remove ${ARCHIVES_DIR} before proceeding." + exit 1 +fi + +mkdir -p "${ARCHIVES_DIR}" +cd "${ARCHIVES_DIR}" + +TARPREFIX="pandora-${PANDORA_VERSION}" +echo "Cloning ${TARPREFIX}" +git clone --recursive --depth=1 --single-branch --branch "${PANDORA_VERSION}" "${PANDORA_URL}" "${PANDORA_VERSION}" + +echo "Creating tar archive..." +cd "${PANDORA_VERSION}" +git archive --prefix="${TARPREFIX}"/ -o "${ARCHIVES_DIR}/${TARPREFIX}.tar" "${PANDORA_VERSION}" +git submodule foreach --recursive \ + "git archive --prefix=${TARPREFIX}/\${displaypath}/ HEAD > ${ARCHIVES_DIR}/tmp.tar && \ + tar --concatenate --file=${ARCHIVES_DIR}/${TARPREFIX}.tar ${ARCHIVES_DIR}/tmp.tar" > /dev/null +rm "${ARCHIVES_DIR}/tmp.tar" + +echo "Compressing to tar.gz..." +gzip -9 "${ARCHIVES_DIR}/${TARPREFIX}.tar" + +echo "Compressing to zip..." +cd "${ARCHIVES_DIR}" && tar xzf "${TARPREFIX}.tar.gz" && \ +zip -r "${TARPREFIX}.zip" "${TARPREFIX}" > /dev/null + +echo "All done!" +######################################################################################################################## diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index e4dabd8c..dbaac2d7 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -16,11 +16,12 @@ target_include_directories(${PROJECT_NAME}_test PUBLIC target_link_libraries(${PROJECT_NAME}_test ${Gtest_LIBRARIES} ${GATB_LIBS} - ${BOOST_LIBRARIES} + ${Boost_LIBRARIES} ${ZLIB_LIBRARY} ${CMAKE_DL_LIBS} ${STATIC_C_CXX} ${BACKWARD_LIBRARIES} - ) + ${RT_LIBRARY} +) add_test(NAME ${PROJECT_NAME}_test COMMAND ${PROJECT_NAME}_test)