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Merge pull request #52 from pachterlab/devel
Merge 0.31.5 into main
2 parents 2bb75cf + e45ee8f commit c8720ca

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11 files changed

+150
-15
lines changed

11 files changed

+150
-15
lines changed

‎func_tests/CMakeLists.txt‎

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@@ -105,3 +105,27 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/smR2.fastq.gz
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_sm.txt
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config.tsv
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_.tsv
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config__.tsv
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config___.tsv
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/input.fastq
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/input_.fastq
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/input__.fastq
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/input___.fastq
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DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
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‎func_tests/config.tsv‎

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groups ids tags distances locations previous
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NYStgBot Y18 TCTCCTTACG 0:0:0 0:0:11 -
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NYStgBot Y32 TGTAGTTCTA 0:1:1 0:0:11 -
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OddBot3 O45 GCCTAGTAGAAGACGTT 2:2:2 0:11:0 {{NYStgBot}}4-10
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EvenBot2 E41 ATAGATTGTTGCGTGCT 2:2:2 0:11:0 {{OddBot3}}4-10
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OddBot2 O21 GGATAGCACCGTTCATT 1:1:1 0:11:0 {{EvenBot2}}4-10
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EvenBot1 E2 TGTAGGTTCTGGAATAT 0:0:0 0:11:0 {{OddBot2}}4-10
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OddBot1 O85 GCTGTGTCTGTCACCT 1:1:1 0:11:0 {{EvenBot1}}4-10
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DPM_const DPM_const TCATGTCTTCCGATCT 2:0:2 0:11:0 {{OddBot1}}4-10
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DPM_R2 DPM1 TGGGTGTTT 1:0:1 0:11:0 {DPM_const}0-0

‎func_tests/config_.tsv‎

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tags locations
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TGTAGG 0:0:0
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TGTAGGTT 0:0:0
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TGGG 0:0:0

‎func_tests/config__.tsv‎

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ids tags distance
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tagT TTT 0
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tagT TTTT 0
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tagT TTTTT 0
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tagT TTTTTT 0
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tagT TTTTTTT 0
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tagT TTTTTTTT 0
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tagT TTTTTTTTT 0
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tagT TTTTTTTTTT 1
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tagT TTTTTTTTTTT 1
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tagT TTTTTTTTTTTT 1
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tagT TTTTTTTTTTTTT 1
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tagT TTTTTTTTTTTTTT 1
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tagT TTTTTTTTTTTTTTT 1
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‎func_tests/config___.tsv‎

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ids tags distance partial5
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tagT TTTTTTTTTT 0 3:0.2
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tagA AAAAAAAAAA 1 3:0.2
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tagG GGGGGGGGGG 1 -
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‎func_tests/input.fastq‎

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@r1
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TCTCCTTACGGACAACTGCCTAGTAGAAGACGTTTGACTTGATAGATTGTTGCGTGCTCACAACTGGATAGCACCGTTCATTTGACTTGTGTAGGTTCTGGAATATGACAACTGCTGTGTCTGTCACCTTTGACTTGTCA
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+
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TCTCCTTACGGACAACTGCCTAGTAGAAGACGTTTGACTTGATAGATTGTTGCGTGCTCACAACTGGATAGCACCGTTCATTTGACTTGTGTAGGTTCTGGAATATGACAACTGCTGTGTCTGTCACCTTTGACTTGTCA

‎func_tests/input_.fastq‎

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@r
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NNNNNNNNNNTGACTTGTGTAGGTTCTGGAAT
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+
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NNNNNNNNNNTGACTTGTGTAGGTTCTGGAAT

‎func_tests/input__.fastq‎

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@11_bp_no_mismatch
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AAATTTTTTTTTTTAAA
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;;;;;;;;;;;;;;;;;
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@11_bp_1_internal_mismatch
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AAATTTTTTTTTCTAAA
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;;;;;;;;;;;;;;;;;
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@11_bp_1_internal_mismatch2
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AAATTTTTTTTCTTAAA
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;;;;;;;;;;;;;;;;;
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@11_bp_1_5prime_mismatch
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AAACTTTTTTTTTTAAA
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;;;;;;;;;;;;;;;;;
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@11_bp_1_3prime_mismatch
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AAATTTTTTTTTTCAAA
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;;;;;;;;;;;;;;;;;
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‎func_tests/input___.fastq‎

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@read1 5prime tagT
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TTTTTTTTTT
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;;;;;;;;;;
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@read2 5prime tagT with 3prime substitution
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TTTTTTTTTC
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;;;;;;;;;;
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@read3 5prime tagT with interior substitution
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TTTCTTTTTT
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;;;;;;;;;;
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@read4 5prime tagT with interior substitution within first 3 bp
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TTCTTTTTTT
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;;;;;;;;;;
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@read5 5prime tagT with interior substitution within first 3 bp
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TCTTTTTTTT
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;;;;;;;;;;
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@read6 5prime tagT with 5prime substitution
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CTTTTTTTTT
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;;;;;;;;;;
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@read7 5prime tagT with 5prime and 3prime substitutions
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CTTTTTTTTC
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;;;;;;;;;;
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@read8 5prime tagT with 5prime and interior substitutions
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CTTTTTTCTT
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;;;;;;;;;;
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@read9 5prime tagA with 5prime and interior substitutions; like read3
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AAACAAAAAA
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;;;;;;;;;;
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@read10 5prime tagG with 5prime and interior substitutions; like read3
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GGGCGGGGGG
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;;;;;;;;;;
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‎func_tests/runtests.sh‎

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@@ -94,16 +94,6 @@ checkcmdoutput "cat $test_dir/mx.txt" b95e8b332c8a0a7ffc0f91118e754302
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checkcmdoutput "$splitcode --assign --x-only --nFastqs=2 --empty N -x \"0:0<R1>0:-1,<R1[10]>{adapter},{adapter}<R1[1-65]>,2:0<R2[1-65]>\" --gzip --mod-names --bclen=20 -t 1 -c $test_dir/config_sm.txt --mapping=/dev/null --pipe $test_dir/smR1.fastq.gz $test_dir/smR2.fastq.gz" 8fc440842f4e2922976cdc1b165008b1
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# Test lift workflow
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_1.vcf.gz CAST_EiJ --kmer-length=31 --kmer-output=$test_dir/test.kmers.1.txt" 7e9c1d67efdf7113bfab367cb5d2d640
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ --rename --kmer-length=31 --kmer-output=$test_dir/test.kmers.2.txt" c9a91833da19b20383d6bd1d3e32ff8f
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checkcmdoutput "cat $test_dir/test.kmers.1.txt" 54d189f4549f6b35ea80ec5c167332b7
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checkcmdoutput "cat $test_dir/test.kmers.2.txt" 9982de087ed358724580836600cc9ba7
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ --diploid --kmer-length=31 --kmer-output=$test_dir/test.kmers.2.txt" 6c33bd3ba7cd9aaefeca5cbaa272cdfe
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checkcmdoutput "cat $test_dir/test.kmers.2.txt" a4c73b67a0ad6e5094ff7f2dfdda15bc
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checkcmdoutput "$splitcode --lift --snv-only $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ" 4bdcaf9f34da45033d477651d8845bf2
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checkcmdoutput "$splitcode --lift --kmer-sj $test_dir/vcf_validation.fa.gz $test_dir/example.SJ.tab --kmer-length=31 --kmer-header=X_ --kmer-header-num" 1e88d0b72323a6c11faa73e19007fc5f
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# Test from-name, random, and revcomp
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cmdexec "wc $test_dir/test_summary.txt"
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checkcmdoutput "$splitcode --trim-only --pipe -q 10 --qtrim-3 --qtrim-pre -5 5 -E ATCG $test_dir/test.fq" 1b5a09bd343382ee78c9aa51245557c2
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# Some fixes (Dec. 2025)
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checkcmdoutput "$splitcode --trim-only --pipe -c $test_dir/config.tsv --loc-names --out-fasta --nFastqs 1 $test_dir/input.fastq" a4508f24c69838b07cec04978def09ca
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checkcmdoutput "$splitcode --trim-only --pipe -c $test_dir/config_.tsv --loc-names --out-fasta --nFastqs 1 $test_dir/input_.fastq" 200fb9106e47c741b1891e4b2fedef05
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checkcmdoutput "$splitcode --trim-only --pipe -c $test_dir/config__.tsv --loc-names --out-fasta --nFastqs 1 $test_dir/input__.fastq" 4caa199550f26000ac787821cc62668c
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checkcmdoutput "$splitcode --trim-only --pipe -c $test_dir/config___.tsv --loc-names --out-fasta --nFastqs 1 $test_dir/input___.fastq" 209698dea910ed4d4cd05dbce0889800
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# Adapter trimming tests
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=3:0.35 --left=1 --pipe $test_dir/test.fq" b637fbabe71eb90bb9b3399a17eabef7
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=3:0.34 --left=1 --pipe $test_dir/test.fq" b637fbabe71eb90bb9b3399a17eabef7
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=3:0.33 --left=1 --pipe $test_dir/test.fq" cb52b79ed7469ca2ffe5739ec544b157
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=4:0.34 --left=1 --pipe $test_dir/test.fq" cb52b79ed7469ca2ffe5739ec544b157
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=2:0.34 --left=1 --pipe $test_dir/test.fq" c6eba12c36e53301f23a9823c2901f24
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checkcmdoutput "$splitcode --trim-only -b CCAAA,CCGGAA --partial5=2:0.34, --partial3=,4 --left=1,0 --right=0,1 --pipe $test_dir/test.fq" 5d4541fb96da328d07ab9189216cf4a5
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checkcmdoutput "$splitcode --trim-only -b CCAAA --partial5=2:0.34 --left=1 --pipe $test_dir/test.fq" b637fbabe71eb90bb9b3399a17eabef7
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checkcmdoutput "$splitcode --trim-only -b CCAAA,CCGGAA --partial5=2:0.34, --partial3=,4 --left=1,0 --right=0,1 --pipe $test_dir/test.fq" 93f1726415edb410d5e733603bc4be11
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checkcmdoutput "$splitcode --trim-only -b CCGC -l 0:-4:0 --partial3=4:0.25 --right=1 --pipe $test_dir/test.fq" 11b55a195b5976331305569416db5bd4
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checkcmdoutput "$splitcode --trim-only -b CCGG,CCGG -i a,b -l 0:-4:9,1:-4:10 --partial3=2,2 --right=1,1 -N 2 --pipe $test_dir/test.fq $test_dir/test.fq" 6807e3ba911fde8fb437f693d055c11f
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checkcmdoutput "$splitcode --trim-only -b CCGC,GAAG -a ,{CCGC} -v {GAAG}, -l 0:-4:0, --partial3=4:0.25,3 --partial5=4,3 --right=1,0 --left=0,1 --pipe $test_dir/test.fq" 93f1726415edb410d5e733603bc4be11
@@ -553,4 +550,14 @@ TATTATGGTCCCCCCCCTTCGTGGAATCTAGCTGACTTGTGACTAGCTDGGGGGGGGGG" > $test_dir/test_te
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checkcmdoutput "$splitcode --assign -m /dev/null --mod-names -g PART,RPM,RPM,ODD,Y -i Part,RTBC2,RTBC4,Odd2Bo1,NYBot1_Stg -b TGACTTG,TTTTTTT,GGGGGGG,TTCGTGGAATCTAGC,TATTATGGT --maxFindsG=Y:1 -p $test_dir/test_term.fq" 79ad1ca9184b274e1396b5f2220cbade
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# Test lift workflow
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_1.vcf.gz CAST_EiJ --kmer-length=31 --kmer-output=$test_dir/test.kmers.1.txt" 7e9c1d67efdf7113bfab367cb5d2d640
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ --rename --kmer-length=31 --kmer-output=$test_dir/test.kmers.2.txt" c9a91833da19b20383d6bd1d3e32ff8f
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checkcmdoutput "cat $test_dir/test.kmers.1.txt" 54d189f4549f6b35ea80ec5c167332b7
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checkcmdoutput "cat $test_dir/test.kmers.2.txt" 9982de087ed358724580836600cc9ba7
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checkcmdoutput "$splitcode --lift $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ --diploid --kmer-length=31 --kmer-output=$test_dir/test.kmers.2.txt" 6c33bd3ba7cd9aaefeca5cbaa272cdfe
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checkcmdoutput "cat $test_dir/test.kmers.2.txt" a4c73b67a0ad6e5094ff7f2dfdda15bc
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checkcmdoutput "$splitcode --lift --snv-only $test_dir/vcf_validation.fa.gz $test_dir/test_2.vcf.gz CAST_EiJ" 4bdcaf9f34da45033d477651d8845bf2
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checkcmdoutput "$splitcode --lift --kmer-sj $test_dir/vcf_validation.fa.gz $test_dir/example.SJ.tab --kmer-length=31 --kmer-header=X_ --kmer-header-num" 1e88d0b72323a6c11faa73e19007fc5f
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