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Test-data
 - updating amplicon - adding shotgun (from V-pipe) - (simple and hackish) test suite
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‎.gitignore

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@@ -20,6 +20,7 @@ install-sh
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missing
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py-compile
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ar-lib
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test-driver
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/shorah
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# generated tarball

‎.travis.yml

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@@ -9,9 +9,10 @@ python:
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before_install:
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- sudo apt-get install -y libhts-dev libboost-math-dev libboost-random-dev autoconf automake pkg-config m4
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- source ~/virtualenv/python3.8/bin/activate
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- pip install Biopython numpy
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compiler:
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- gcc
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before_script: autoreconf -vif
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before_script: autoreconf -vif -I m4
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script: ./configure && make -j1 distcheck

‎Makefile.am

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@@ -55,7 +55,43 @@ dist_ampliconpkgdata_DATA = \
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examples/amplicon_test/README.md \
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examples/amplicon_test/ampli_sorted.bam \
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examples/amplicon_test/amplicon_reads.fastq \
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examples/amplicon_test/reference.fasta
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examples/amplicon_test/reference.fasta \
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examples/amplicon_test/amplicon_test
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shotgunpkgdatadir = $(pkgdatadir)/shotgun_test
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dist_shotgunpkgdata_DATA = \
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examples/shotgun_test/README.md \
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examples/shotgun_test/test_aln.cram \
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examples/shotgun_test/test_ref.fasta \
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examples/shotgun_test/test.csv \
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examples/shotgun_test/shotgun_test
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# tests
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dist_check_DATA = \
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examples/run_end2end_test \
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$(dist_ampliconpkgdata_DATA) \
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$(dist_shotgunpkgdata_DATA)
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AM_TESTS_ENVIRONMENT = \
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export PYTHONPATH='$(realpath $(top_srcdir)/src)'; \
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export PATH="$(realpath $(builddir)/):$(PATH)";
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TESTS = examples/amplicon_test/amplicon_test \
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examples/shotgun_test/shotgun_test \
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examples/shotgun_test/test.csv
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examples/shotgun_test/test.log: examples/shotgun_test/shotgun_test.log
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TEST_EXTENSIONS = .csv
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CSV_LOG_COMPILER = diff
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AM_CSV_LOG_FLAGS = -u $(builddir)/shotgun_test/snv/SNVs_0.010000_final.csv
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# NOTE cheating by considering the data files as test (normally it should be wraping scripts, see next)
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LOG_COMPILER = $(top_srcdir)/examples/run_end2end_test
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AM_LOG_FLAGS = $(PYTHON)
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# add test files to cleanup
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clean-local:
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-rm -rf amplicon_test/ shotgun_test/
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# version handling
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$(top_srcdir)/.version:

‎configure.ac

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@@ -23,7 +23,7 @@ AC_PREREQ([2.69])
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AC_INIT(
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[shorah],
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m4_esyscmd([build-aux/git-version-gen .tarball-version]),
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[[email protected]])
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[[email protected]])
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AC_CONFIG_SRCDIR([src/cpp/dpm_sampler.cpp])
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AC_CONFIG_MACRO_DIR([m4])
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‎examples/amplicon_test/README.md

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### Sample files to test `amplian.py`
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### Sample files to test `shorah amplicon`
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Use files in this directory to test shorah in amplicon mode.
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The sorted bam file has been obtained from the reads with
@@ -10,8 +10,9 @@ sort the alignment. The commands given are
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[user@host amplicon_test]$ smalt map -f sam -o ampli.sam ref amplicon_reads.fastq
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[user@host amplicon_test]$ samtools view -S -b ampli.sam | samtools sort - ampli_sorted
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You can then run `amplian` as follows
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[user@host amplicon_test]$ amplian.py -b ampli_sorted.bam -f reference.fasta
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You can then run `shorah amplicon` as follows
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[user@host amplicon_test]$ shorah amplicon -b ampli_sorted.bam -f reference.fasta
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Some warning will be raised. The output files will be `SNV.txt` and `SNVs_0.010000_final.csv`.
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Only SNVs exceeding the threshold of 5% are returned (see [paper](http://www.biomedcentral.com/1471-2164/14/501)).
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----
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`amplian` is still under development and thus should be considered in
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beta more than the rest of ShoRAH (say, alpha).
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`shorah amplicon` is still under development.

‎examples/amplicon_test/amplicon_test

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shorah amplicon -f reference.fasta -b ampli_sorted.bam

‎examples/run_end2end_test

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#!/bin/bash
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interpreter="$1"
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test="$2"
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testscript="$(<"${test}")"
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testdir="$(dirname "${test}")"
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testname="$(basename "${testdir}")"
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mkdir -p "${testname}"
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cp "${testdir}"/*.*am "${testdir}"/*ref*.fas* "${testname}"/
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cd "${testname}"/
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echo -e "pyton:\t${PYTHONPATH}"
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echo -e "path:\t${PATH}"
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echo -e "test:\t${interpreter} ../${testscript}"
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${interpreter} ../${testscript}
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status=$?
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echo -e "\nstatus:${status}\nshorah.log:"
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[ -e shorah.log ] && cat shorah.log
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exit ${status}

‎examples/shotgun_test/README.md

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### Sample files to test `shorah shotgun`
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Use files in this directory to test shorah in shotgun mode.
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The reads data comes from the
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[test-data](https://github.com/cbg-ethz/V-pipe/tree/master/testdata/2VM-sim/20170904/raw_data)
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of [V-pipe](https://cbg-ethz.github.io/V-pipe/)
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and has been processed with the pipeline using the `bwa`
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[option](https://github.com/cbg-ethz/V-pipe/wiki/options#aligner):
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```ini
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[general]
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aligner = bwa
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```
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The sorted bam file has been further compressed with samtools for space saving:
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[user@host shotgun_test]$ samtools view -T test_ref.fasta -C -O cram,embed_ref,use_bzip2,use_lzma,level=9,seqs_per_slice=1000000 -o test_aln.cram V-pipe/work/samples/2VM-sim/20170904/alignments/REF_aln.bam
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You can then run `shorah shotgun` as follows
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[user@host shotgun_test]$ shorah shotgun -b test_aln.cram -f test_ref.fasta
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The output files will be `snv/SNVs_0.010000_final.vcf` and `snv/SNVs_0.010000_final.csv`.

‎examples/shotgun_test/shotgun_test

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shorah shotgun -a 0.1 -w 201 -x 100000 -p 0.9 -c 0 -r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram

‎examples/shotgun_test/test.csv

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Chromosome,Pos,Ref,Var,Frq1,Frq2,Frq3,Pst1,Pst2,Pst3,Fvar,Rvar,Ftot,Rtot,Pval,Qval
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HXB2,2357,A,C,*,0.4619,0.5185,*,1.0000,1.0000,37,2,81,6,1,1
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HXB2,2361,A,G,*,0.4619,0.5185,*,1.0000,1.0000,37,3,88,7,1,1
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HXB2,2362,G,A,*,1.0000,1.0000,*,1.0000,1.0000,86,6,88,7,1,1
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HXB2,2363,T,G,*,0.4619,0.5185,*,1.0000,1.0000,38,2,89,7,0.935492,1
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HXB2,2372,A,G,*,0.4619,0.5185,*,1.0000,1.0000,55,7,106,12,0.87041,1
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HXB2,2432,T,G,0.4619,0.5185,0.5483,1.0000,1.0000,1.0000,85,20,163,36,0.882883,1
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HXB2,2439,C,G,0.4619,0.5185,0.5483,1.0000,1.0000,1.0000,86,20,172,37,0.850419,1
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HXB2,2440,T,A,0.4619,0.5185,0.5483,1.0000,1.0000,1.0000,86,20,174,37,0.825422,1
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HXB2,2453,T,C,0.5381,0.4815,0.4517,1.0000,1.0000,1.0000,93,19,188,44,0.813301,1
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HXB2,2467,T,A,0.4619,0.5185,0.5483,1.0000,1.0000,1.0000,102,30,206,56,0.821381,1
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HXB2,2534,T,C,0.4815,0.4517,0.5856,1.0000,1.0000,1.0000,112,56,213,110,0.961894,1
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HXB2,2558,C,T,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,214,124,214,125,1,1
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HXB2,2567,G,A,0.5483,0.4144,0.4353,1.0000,1.0000,1.0000,97,62,214,130,0.872744,1
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HXB2,2603,C,T,0.4144,0.4353,0.4792,1.0000,1.0000,1.0000,93,68,210,149,0.937209,1
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HXB2,2612,T,G,0.4144,0.4353,0.4792,1.0000,1.0000,1.0000,101,67,219,151,0.929187,1
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HXB2,2669,G,A,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,214,162,215,163,1,1
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HXB2,2684,G,A,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,213,165,214,167,0.999687,1
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HXB2,2708,A,G,0.4353,0.4792,0.5094,1.0000,1.0000,1.0000,107,63,213,155,0.446817,1
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HXB2,2801,T,C,0.4792,0.5094,0.4937,1.0000,1.0000,1.0000,119,88,237,188,0.812717,1
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HXB2,2807,C,T,0.4906,0.5063,0.5381,1.0000,1.0000,1.0000,111,102,230,198,0.814688,1
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HXB2,2828,A,C,0.5094,0.4937,0.4619,1.0000,1.0000,1.0000,118,103,224,207,0.845057,1
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HXB2,2840,C,T,0.4906,0.5063,0.5381,1.0000,1.0000,1.0000,113,106,230,209,0.922908,1
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HXB2,2853,A,C,0.4906,0.5063,0.5381,1.0000,1.0000,1.0000,113,105,228,214,0.998846,1
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HXB2,2885,T,C,0.5063,0.5381,0.4974,1.0000,1.0000,1.0000,115,107,223,223,0.793957,1
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HXB2,2913,G,A,0.5063,0.5381,0.4974,1.0000,1.0000,1.0000,117,113,221,238,0.674808,1
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HXB2,2930,T,C,0.4937,0.4619,0.5026,1.0000,1.0000,1.0000,105,126,219,236,0.682947,1
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HXB2,2984,G,A,0.4619,0.5026,0.5247,1.0000,1.0000,1.0000,101,113,213,220,0.772415,1
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HXB2,3032,A,G,0.4974,0.4753,0.5509,1.0000,1.0000,1.0000,117,105,216,224,0.573896,1
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HXB2,3033,A,T,0.4974,0.4753,0.5509,1.0000,1.0000,1.0000,116,104,215,221,0.597216,1
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HXB2,3107,T,C,0.5247,0.4491,0.5278,1.0000,1.0000,1.0000,120,118,238,235,1,1
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HXB2,3147,A,G,0.4491,0.5278,0.4567,1.0000,1.0000,1.0000,114,105,238,226,0.931115,1
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HXB2,3161,G,A,0.5509,0.4722,0.5433,1.0000,1.0000,1.0000,123,121,234,228,0.99466,1
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HXB2,3161,G,T,0.4491,0.5278,0.4567,1.0000,1.0000,1.0000,110,107,234,228,1,1
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HXB2,3181,G,A,0.4491,0.5278,0.4567,1.0000,1.0000,1.0000,112,103,243,218,0.946285,1
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HXB2,3188,A,G,0.4491,0.5278,0.4567,1.0000,1.0000,1.0000,110,101,238,220,1,1
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HXB2,3189,C,T,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,233,224,237,224,0.952959,1
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HXB2,3230,C,T,0.5278,0.4567,0.5057,1.0000,1.0000,1.0000,113,109,226,237,0.75634,1
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HXB2,3285,C,T,0.4567,0.5057,0.5461,1.0000,1.0000,1.0000,108,112,213,237,0.79725,1
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HXB2,3296,A,G,0.5433,0.4943,0.4539,1.0000,1.0000,1.0000,105,126,211,239,0.842019,1
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HXB2,3317,C,T,0.4567,0.5057,0.5461,1.0000,1.0000,1.0000,98,118,198,241,0.989848,1
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HXB2,3326,G,A,0.5433,0.4943,0.4539,1.0000,1.0000,1.0000,95,113,194,236,0.953125,1
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HXB2,3335,G,A,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,194,229,196,231,1,1
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HXB2,3362,C,T,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,182,220,182,222,0.980391,1
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HXB2,3363,C,G,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,182,222,184,222,0.984006,1
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HXB2,3379,G,A,0.5057,0.5461,0.5636,1.0000,1.0000,1.0000,102,119,188,229,0.883204,1
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HXB2,3395,C,T,0.4943,0.4539,0.4364,1.0000,1.0000,1.0000,85,108,186,229,0.938325,1
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HXB2,3401,A,G,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,180,225,182,227,1,1
49+
HXB2,3426,A,G,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,171,219,175,224,1,1
50+
HXB2,3470,A,G,1.0000,1.0000,1.0000,1.0000,1.0000,1.0000,174,212,175,214,1,1
51+
HXB2,3488,A,G,0.4364,0.5038,0.4627,1.0000,1.0000,1.0000,74,100,167,214,0.877264,1
52+
HXB2,3513,T,A,0.5636,0.4962,0.5373,1.0000,1.0000,1.0000,89,104,156,204,0.674697,1
53+
HXB2,3533,A,G,0.5636,0.4962,0.5373,1.0000,1.0000,1.0000,80,95,143,202,0.51546,1
54+
HXB2,3534,A,C,0.5636,0.4962,0.5373,1.0000,1.0000,1.0000,80,95,142,202,0.497737,1
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HXB2,3551,A,G,0.4962,0.5373,0.5711,1.0000,1.0000,1.0000,77,111,136,222,0.643757,1
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HXB2,3578,A,G,0.4962,0.5373,0.5711,1.0000,1.0000,1.0000,69,117,115,231,0.529331,1
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HXB2,3586,T,A,0.4962,0.5373,0.5711,1.0000,1.0000,1.0000,63,118,108,228,0.666343,1
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HXB2,3608,A,G,0.4627,0.4289,0.3914,1.0000,1.0000,1.0000,36,116,91,232,0.482916,1
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HXB2,3622,G,A,0.4627,0.4289,0.3914,1.0000,1.0000,1.0000,32,106,84,226,0.559109,1
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HXB2,3644,A,G,0.4627,0.4289,0.3914,1.0000,1.0000,1.0000,25,98,67,217,0.640733,1
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HXB2,3665,G,A,0.4627,0.4289,0.3914,1.0000,1.0000,1.0000,18,89,54,202,0.520521,1
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HXB2,3675,A,G,1.0000,1.0000,-,1.0000,1.0000,-,47,196,47,197,0.979302,1
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HXB2,3720,C,T,0.4289,0.3914,-,1.0000,1.0000,-,7,62,23,150,0.695544,1
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HXB2,3722,G,A,1.0000,1.0000,-,1.0000,1.0000,-,21,148,22,148,1,1.0
65+
HXB2,3728,A,T,0.5711,0.6086,-,1.0000,1.0000,-,16,84,22,145,0.585861,1

‎examples/shotgun_test/test_aln.cram

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‎examples/shotgun_test/test_ref.fasta

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>HXB2
2+
TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA

‎src/shorah/cli.py

+2-1
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,8 @@
5555
try:
5656
__version__ = get_distribution('shorah').version
5757
except DistributionNotFound:
58-
print("your message", file=sys.stderr)
58+
__version__ = 'unknown'
59+
print("cannot find version", file=sys.stderr)
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# manipulate path to import functions
6162
parent_dir = os.path.join(base_dir, 'src')

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