From 6fe18f456b1a91eb8f4a785a678160751e2a19e8 Mon Sep 17 00:00:00 2001
From: Leandro Ishi <leandro.ishi.lima@gmail.com>
Date: Wed, 12 May 2021 15:18:44 +0100
Subject: [PATCH 1/5] Adding infrastructure for conda build

---
 .gitignore                   |  2 ++
 CMakeLists.txt               | 19 +++++++++----
 example/run_pandora_conda.sh | 39 ++++++++++++++++++++++++++
 scripts/create_archives.sh   | 54 ++++++++++++++++++++++++++++++++++++
 test/CMakeLists.txt          |  5 ++--
 5 files changed, 112 insertions(+), 7 deletions(-)
 create mode 100755 example/run_pandora_conda.sh
 create mode 100644 scripts/create_archives.sh

diff --git a/.gitignore b/.gitignore
index fede8a6e..18bf813d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -99,3 +99,5 @@ pandora
 #portable binary build dir
 build_portable_executable
 pandora-linux-precompiled
+
+/archives/
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ba25ed1f..53efa89c 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 ${CMAKE_BINARY_DIR}/hunter)
 include("cmake/HunterGate.cmake")
 HunterGate(
@@ -55,8 +56,13 @@ else ()
     set(CMAKE_CXX_FLAGS "${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/example/run_pandora_conda.sh b/example/run_pandora_conda.sh
new file mode 100755
index 00000000..b765c577
--- /dev/null
+++ b/example/run_pandora_conda.sh
@@ -0,0 +1,39 @@
+#!/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"
+
+
+function download_tool {
+  URL=$1
+  executable=$2
+  wget "${URL}" -O "${executable}"
+  chmod +x "${executable}"
+}
+
+download_tool "${pandora_URL}" "${pandora_executable}"
+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
+echo "Running ${pandora_executable} index"
+"${pandora_executable}" index 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
+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
+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
+echo "Running ${pandora_executable} index on updated PRGs"
+"${pandora_executable}" index 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
+echo "Running pandora with denovo - done!"
diff --git a/scripts/create_archives.sh b/scripts/create_archives.sh
new file mode 100644
index 00000000..3991dea0
--- /dev/null
+++ b/scripts/create_archives.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+# run from project root: scripts/create_archives.sh <PANDORA_VERSION>
+# 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 <PANDORA_VERSION>"
+    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)

From dd5b4e8f0e1ae028215dce62d13c2486ea74e971 Mon Sep 17 00:00:00 2001
From: Leandro Ishi <leandro.ishi.lima@gmail.com>
Date: Mon, 17 May 2021 23:14:09 +0100
Subject: [PATCH 2/5] Updating example with a self check

---
 .gitignore                                    |    3 +-
 example/README.md                             |   20 +-
 .../toy_sample_1/kmer_covgs.txt               | 1000 +++++++++++++++++
 .../toy_sample_1/kmer_probs.txt               |  200 ++++
 .../toy_sample_1/pandora.consensus.fq.gz      |  Bin 0 -> 368 bytes
 .../toy_sample_1/pandora.pangraph.gfa         |    3 +
 .../toy_sample_2/kmer_covgs.txt               | 1000 +++++++++++++++++
 .../toy_sample_2/kmer_probs.txt               |  200 ++++
 .../toy_sample_2/pandora.consensus.fq.gz      |  Bin 0 -> 370 bytes
 .../toy_sample_2/pandora.pangraph.gfa         |    3 +
 .../toy_sample_1/kmer_covgs.txt               | 1000 +++++++++++++++++
 .../toy_sample_1/kmer_probs.txt               |  200 ++++
 .../toy_sample_1/pandora.consensus.fq.gz      |  Bin 0 -> 368 bytes
 .../toy_sample_1/pandora.pangraph.gfa         |    3 +
 .../toy_sample_2/kmer_covgs.txt               | 1000 +++++++++++++++++
 .../toy_sample_2/kmer_probs.txt               |  200 ++++
 .../toy_sample_2/pandora.consensus.fq.gz      |  Bin 0 -> 371 bytes
 .../toy_sample_2/pandora.pangraph.gfa         |    3 +
 .../pandora_discover_out/denovo_paths.txt     |   34 +
 .../toy_sample_1/denovo_paths.txt             |   16 +
 .../toy_sample_1/pandora.consensus.fq.gz      |  Bin 0 -> 368 bytes
 .../toy_sample_1/pandora.pangraph.gfa         |    3 +
 .../candidate_regions_write_buffer.bin        |   10 +
 .../toy_sample_2/denovo_paths.txt             |   17 +
 .../toy_sample_2/pandora.consensus.fq.gz      |  Bin 0 -> 370 bytes
 .../toy_sample_2/pandora.pangraph.gfa         |    3 +
 .../candidate_regions_write_buffer.bin        |   12 +
 .../prgs/kmer_prgs/01/GC00006032.k15.w14.gfa  |   97 ++
 .../prgs/kmer_prgs/01/GC00010897.k15.w14.gfa  |  146 +++
 .../prgs/pangenome.prg.fa.k15.w14.idx         |  113 ++
 example/out_truth/prgs/pangenome.update_DS    |  Bin 0 -> 510 bytes
 .../ForkPoolWorker-1/GC00006032.fa.pickle     |  Bin 0 -> 48037 bytes
 .../ForkPoolWorker-1/GC00010897.fa.pickle     |  Bin 0 -> 19895 bytes
 .../kmer_prgs/01/GC00006032.k15.w14.gfa       |  102 ++
 .../kmer_prgs/01/GC00010897.k15.w14.gfa       |  158 +++
 .../pangenome_updated.prg.fa.k15.w14.idx      |  120 ++
 example/run_pandora.sh                        |   20 +-
 37 files changed, 5672 insertions(+), 14 deletions(-)
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_covgs.txt
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_probs.txt
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.pangraph.gfa
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_covgs.txt
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_probs.txt
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.pangraph.gfa
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_covgs.txt
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_probs.txt
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.pangraph.gfa
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_covgs.txt
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_probs.txt
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/output_toy_example_with_denovo/toy_sample_2/pandora.pangraph.gfa
 create mode 100644 example/out_truth/pandora_discover_out/denovo_paths.txt
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_1/denovo_paths.txt
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_1/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_1/pandora.pangraph.gfa
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_1/temp_child_00/candidate_regions_write_buffer.bin
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_2/denovo_paths.txt
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_2/pandora.consensus.fq.gz
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_2/pandora.pangraph.gfa
 create mode 100644 example/out_truth/pandora_discover_out/toy_sample_2/temp_child_00/candidate_regions_write_buffer.bin
 create mode 100644 example/out_truth/prgs/kmer_prgs/01/GC00006032.k15.w14.gfa
 create mode 100644 example/out_truth/prgs/kmer_prgs/01/GC00010897.k15.w14.gfa
 create mode 100644 example/out_truth/prgs/pangenome.prg.fa.k15.w14.idx
 create mode 100644 example/out_truth/prgs/pangenome.update_DS
 create mode 100644 example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00006032.fa.pickle
 create mode 100644 example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00010897.fa.pickle
 create mode 100644 example/out_truth/updated_prgs/kmer_prgs/01/GC00006032.k15.w14.gfa
 create mode 100644 example/out_truth/updated_prgs/kmer_prgs/01/GC00010897.k15.w14.gfa
 create mode 100644 example/out_truth/updated_prgs/pangenome_updated.prg.fa.k15.w14.idx

diff --git a/.gitignore b/.gitignore
index 18bf813d..2919e2b1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -100,4 +100,5 @@ pandora
 build_portable_executable
 pandora-linux-precompiled
 
-/archives/
\ No newline at end of file
+/archives/
+/example/out/
diff --git a/example/README.md b/example/README.md
index 67a13c77..6c23cd80 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
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	0
+3	0
+4	1
+5	1
+6	1
+7	0
+8	1
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diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_probs.txt b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/kmer_probs.txt
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diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.consensus.fq.gz b/example/out_truth/output_toy_example_no_denovo/toy_sample_1/pandora.consensus.fq.gz
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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
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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
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diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_probs.txt b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/kmer_probs.txt
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diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.consensus.fq.gz b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.consensus.fq.gz
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diff --git a/example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.pangraph.gfa b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.pangraph.gfa
new file mode 100644
index 00000000..2ae02629
--- /dev/null
+++ b/example/out_truth/output_toy_example_no_denovo/toy_sample_2/pandora.pangraph.gfa
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diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_covgs.txt b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_covgs.txt
new file mode 100644
index 00000000..a7828b78
--- /dev/null
+++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_covgs.txt
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diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_probs.txt b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/kmer_probs.txt
new file mode 100644
index 00000000..cd818069
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diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.consensus.fq.gz b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.consensus.fq.gz
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diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.pangraph.gfa b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.pangraph.gfa
new file mode 100644
index 00000000..e775e410
--- /dev/null
+++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_1/pandora.pangraph.gfa
@@ -0,0 +1,3 @@
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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
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diff --git a/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_probs.txt b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_probs.txt
new file mode 100644
index 00000000..7b937e43
--- /dev/null
+++ b/example/out_truth/output_toy_example_with_denovo/toy_sample_2/kmer_probs.txt
@@ -0,0 +1,200 @@
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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 0000000000000000000000000000000000000000..33d871767641834f60f011f73152ca37bf0cf899
GIT binary patch
literal 371
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R|5~|&bYJc5R<YCt001@bt&acz

literal 0
HcmV?d00001

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 0000000000000000000000000000000000000000..3d6a43cafc80ca61ef1d1c929aecc3a3590abd8a
GIT binary patch
literal 368
zcmV-$0gwJ4iwFP!00000|Ls#bP6JU4?dKGs10m2%0$B>AST5XB_yQ3`G$;rG9f#*F
zQK&co0?$a}@$&3%zrU><A<J<wpFO`k&F;@1ckjE;xBctK{_wEBxVyT&zL_sJ(_-kZ
zs18U*bW#dWckl`7#Tfii5JOGTmHaeb#KVD~qCq~O%9VP6klEG7&<iJnTE&xjv?b$`
zvBreMKKzGrnUt=}j*Y~kslMdwQXT}I3mq2qrjzz5tB1?s>~G7k6<MZny;=Q8mgTgb
zHmiY~=3WDwD9*L8mMl-23#DI6#Q3#ZO+6Up9VRlWvxJjWL)`F=O6==!UX>P@^j0X9
zG2AH?(M^!(gzIIBL5g`t-5h2zHIPfCqpTQ#lub7YJGnygqC10-YTsxI)6qlcCx{8A
z%j2=62SXT9S0`>Bo)tX+msX<mQzdt5qih^RIVEK&O<7auV<dZuBfesF0c6lM_-FdB
Omf;IX9+;cd1pojEIk9K}

literal 0
HcmV?d00001

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 0000000000000000000000000000000000000000..17f747c4c9a137bb417af4ee8db026e711f61486
GIT binary patch
literal 370
zcmV-&0ge72iwFP!00000|Ls#dP6JU4?DrI*10hf#gd_!0EEgj>3SS_Chz5ZW&~bQX
z#!sQ*00_J*t)D+*KYMnIoKvpni_6*5%j4|s_+j_H`+VEKe(ay`_a`@J%k$-W!H}s6
zfeK1SR7$|7D)fYOD268qW28A6sZa4`JRLkh2K$I=SNb7BW}zCxFP#c17f<EM#$u^1
z3Ij8;eLRPAm6Tmq9XFDSru(w9U_XVO8=aQEgN=u*nog&qzb(_&WVx8HH>)4Xvbb7Z
zEjN=kt-S`<1kDv(OQI*Oh4$cO(I%n5W<!o0CNsEV7$>EMxzRg<*;mnd2`@0^^--MQ
z`o&l(rkf$ziPnn)2$YA`o5M<$Msm4ypp`}tWwV<U|Ck{1vbzQm)xOaj=BtPAZxBJi
zKTnS(doY4Ab$#Q~<wtD{DBXVOhf3XP8*S4d&?#vPJY`RzMx+UEd{@y1Vi^1z{4@R6
Q$}MI30?wNdZqx+;05C(Wr~m)}

literal 0
HcmV?d00001

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
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+L	41	+	43	+	0M
+L	41	+	44	+	0M
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+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
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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
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+L	3	+	4	+	0M
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+L	4	+	5	+	0M
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+L	5	+	6	+	0M
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+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
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+L	10	+	11	+	0M
+S	11	1{[68, 83)}	FC:i:0		RC:i:0
+L	11	+	12	+	0M
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+L	13	+	14	+	0M
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+L	14	+	15	+	0M
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+L	16	+	17	+	0M
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+L	17	+	19	+	0M
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+L	18	+	20	+	0M
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+L	25	+	26	+	0M
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+L	30	+	31	+	0M
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+L	33	+	34	+	0M
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+L	34	+	35	+	0M
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+L	35	+	36	+	0M
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+L	36	+	37	+	0M
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+L	37	+	38	+	0M
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+L	38	+	39	+	0M
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+L	39	+	40	+	0M
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+L	40	+	41	+	0M
+S	41	1{[273, 288)}	FC:i:0		RC:i:0
+L	41	+	42	+	0M
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+L	42	+	43	+	0M
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+L	43	+	44	+	0M
+L	43	+	45	+	0M
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+L	46	+	48	+	0M
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+L	47	+	49	+	0M
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+L	48	+	49	+	0M
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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 @@
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diff --git a/example/out_truth/prgs/pangenome.update_DS b/example/out_truth/prgs/pangenome.update_DS
new file mode 100644
index 0000000000000000000000000000000000000000..306bb342b350c1b72842f50bf4d649673df06786
GIT binary patch
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diff --git a/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00006032.fa.pickle b/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00006032.fa.pickle
new file mode 100644
index 0000000000000000000000000000000000000000..8fc00631ccfc2216c53cfdc1fb3f5abe41cb6582
GIT binary patch
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diff --git a/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00010897.fa.pickle b/example/out_truth/prgs/pangenome_prgs/ForkPoolWorker-1/GC00010897.fa.pickle
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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 @@
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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 @@
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+L	56	+	58	+	0M
+S	57	1{[389, 404)}	FC:i:0		RC:i:0
+L	57	+	59	+	0M
+S	58	3{[366, 373)[382, 383)[387, 394)}	FC:i:0		RC:i:0
+L	58	+	57	+	0M
+S	59	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)
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+158006043	1	(1, 1{[233, 248)}, 37, 1)
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+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)
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+32446550	1	(1, 1{[29, 44)}, 5, 1)
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+117410367	1	(1, 1{[10, 25)}, 2, 0)
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+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)
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+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)
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+47369520	1	(0, 1{[272, 287)}, 40, 1)
+57951963	1	(0, 1{[262, 277)}, 39, 0)
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+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)
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+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..6ec0fa95 100755
--- a/example/run_pandora.sh
+++ b/example/run_pandora.sh
@@ -20,20 +20,26 @@ 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

From ac6c2de4172498889184bed83aab96be6714b163 Mon Sep 17 00:00:00 2001
From: Leandro Ishi <leandro.ishi.lima@gmail.com>
Date: Fri, 21 May 2021 12:59:47 +0100
Subject: [PATCH 3/5] Updating example to run with pandora installed through
 conda

---
 example/README.md            | 13 ++++++++++++
 example/run_pandora.sh       | 28 +++++++++++++++++++-------
 example/run_pandora_conda.sh | 39 ------------------------------------
 3 files changed, 34 insertions(+), 46 deletions(-)
 delete mode 100755 example/run_pandora_conda.sh

diff --git a/example/README.md b/example/README.md
index 6c23cd80..0c6781a5 100644
--- a/example/README.md
+++ b/example/README.md
@@ -81,6 +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.
+
 <!--Link References-->
 
 [pandora_2020_paper]: https://www.biorxiv.org/content/10.1101/2020.11.12.380378v2
diff --git a/example/run_pandora.sh b/example/run_pandora.sh
index 6ec0fa95..e7775291 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=$1
@@ -15,7 +17,19 @@ function download_tool {
   chmod +x "${executable}"
 }
 
-download_tool "${pandora_URL}" "${pandora_executable}"
+# setup tools
+if [ "$#" -eq 0 ] ; then
+  # not conda env
+  pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0"
+  pandora_executable="./pandora-linux-precompiled-v0.9.0"
+  download_tool "${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..."
diff --git a/example/run_pandora_conda.sh b/example/run_pandora_conda.sh
deleted file mode 100755
index b765c577..00000000
--- a/example/run_pandora_conda.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/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"
-
-
-function download_tool {
-  URL=$1
-  executable=$2
-  wget "${URL}" -O "${executable}"
-  chmod +x "${executable}"
-}
-
-download_tool "${pandora_URL}" "${pandora_executable}"
-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
-echo "Running ${pandora_executable} index"
-"${pandora_executable}" index 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
-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
-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
-echo "Running ${pandora_executable} index on updated PRGs"
-"${pandora_executable}" index 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
-echo "Running pandora with denovo - done!"

From 9a9d3fa6c87251a6783ccdfab4fd29a4d8052080 Mon Sep 17 00:00:00 2001
From: Leandro Ishi <leandro.ishi.lima@gmail.com>
Date: Fri, 21 May 2021 13:18:48 +0100
Subject: [PATCH 4/5] Preparing release 0.9.1

---
 CHANGELOG.md           | 13 ++++++++++++-
 CMakeLists.txt         |  2 +-
 README.md              | 14 +++++++++++---
 example/run_pandora.sh |  4 ++--
 4 files changed, 26 insertions(+), 7 deletions(-)

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 53efa89c..47e29d1a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,7 +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 )
 
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/run_pandora.sh b/example/run_pandora.sh
index e7775291..e2d1284e 100755
--- a/example/run_pandora.sh
+++ b/example/run_pandora.sh
@@ -20,8 +20,8 @@ function download_tool {
 # setup tools
 if [ "$#" -eq 0 ] ; then
   # not conda env
-  pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.0/pandora-linux-precompiled-v0.9.0"
-  pandora_executable="./pandora-linux-precompiled-v0.9.0"
+  pandora_URL="https://github.com/rmcolq/pandora/releases/download/0.9.1/pandora-linux-precompiled-v0.9.1"
+  pandora_executable="./pandora-linux-precompiled-v0.9.1"
   download_tool "${pandora_URL}" "${pandora_executable}"
 else
   # conda env

From 1ce9358a05d904594ebb3cf86fa47239431648bd Mon Sep 17 00:00:00 2001
From: Leandro Ishi <leandro.ishi.lima@gmail.com>
Date: Fri, 21 May 2021 13:31:25 +0100
Subject: [PATCH 5/5] Making create_archives.sh executable

---
 scripts/create_archives.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 scripts/create_archives.sh

diff --git a/scripts/create_archives.sh b/scripts/create_archives.sh
old mode 100644
new mode 100755