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Merge branch 'dev' into meth
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hasindu2008 committed Mar 5, 2024
2 parents ca22a29 + fd44380 commit a2ec103
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -42,7 +42,7 @@ After getting the basic *ssssim* implemented in ~8 hours and successfully baseca
For x86-64 Linux, you can use the precompiled binaries under [releases](https://github.com/hasindu2008/squigulator/releases):

```
VERSION=0.2.2-dirty
VERSION=0.3.0-dirty
wget https://github.com/hasindu2008/squigulator/releases/download/v${VERSION}/squigulator-v${VERSION}-x86_64-linux-binaries.tar.gz
tar xf squigulator-v${VERSION}-x86_64-linux-binaries.tar.gz && cd squigulator-v${VERSION}
./squigulator --help
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2 changes: 1 addition & 1 deletion docs/man.md
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Expand Up @@ -31,7 +31,7 @@ Advanced options are as below:
- `--paf-ref`: in paf output, use the reference as the target instead of read (needs -c)
- `--cdna`: generate cDNA reads (only valid with dna profiles and the reference must a transcriptome, experimental)
- `--trans-count FILE`: simulate relative abundance using specified 2-column tsv with first column containing transcript name and the second containing the count (only for direct-rna and cDNA, experimental). You may generate this a test fatq dataset using minimap2, for example, `minimap2 -cx map-ont transcripts.fa reads.fastq --secondary=no -t20 -uf | cut -f 6 | sort | uniq -c | awk '{print$2"\t"$1}'`.
- `--trans-trunc=yes/no`: simulate transcript truncation (only for direct-rna and cDNA, experimental) [default: no]
- `--trans-trunc=yes/no`: simulate transcript truncation (only for direct-rna, experimental) [default: no]

Developer options (which are not much tested and error handling) are as below:

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7 changes: 6 additions & 1 deletion src/sim.c
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Expand Up @@ -738,7 +738,7 @@ static void print_help(FILE *fp_help, opt_t opt, profile_t p, int64_t nreads) {
fprintf(fp_help," --paf-ref in paf output, use the reference as the target instead of read (needs -c)\n");
fprintf(fp_help," --cdna generate cDNA reads (only valid with dna profiles and the reference must a transcriptome, experimental)\n");
fprintf(fp_help," --trans-count FILE simulate relative abundance using specified tsv with transcript name & count (only for direct-rna and cDNA, experimental)\n");
fprintf(fp_help," --trans-trunc=yes/no simulate transcript truncattion (only for direct-rna and cDNA, experimental) [no]\n");
fprintf(fp_help," --trans-trunc=yes/no simulate transcript truncattion (only for direct-rna, experimental) [no]\n");
fprintf(fp_help," --meth-freq FILE simulate CpG methylation using specified frequency file, tsv file with chr, 0-based pos and freq as the columns (only for DNA, experimental)\n");

fprintf(fp_help,"\ndeveloper options (not much tested yet):\n");
Expand Down Expand Up @@ -993,6 +993,11 @@ int sim_main(int argc, char* argv[], double realtime0) {
//check args
check_args(opt_gvn, rna, opt, paf);

if((opt.flag & SQ_CDNA) && (opt.flag & SQ_TRANS_TRUNC)){
ERROR("%s","Option --trans-trunc is not yet implemnted for --cdna.");
exit(EXIT_FAILURE);
}

if((opt.flag & SQ_CDNA) && (opt.flag & SQ_PREFIX)){
ERROR("%s","Option --prefix is not yet implemnted for --cdna.");
exit(EXIT_FAILURE);
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2 changes: 1 addition & 1 deletion src/version.h
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@@ -1 +1 @@
#define SQ_VERSION "0.2.2-dirty"
#define SQ_VERSION "0.3.0-dirty"
2 changes: 1 addition & 1 deletion test/dna_r10_paf-ref.sam.exp

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2 changes: 1 addition & 1 deletion test/rna_paf.sam.exp
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Expand Up @@ -158,5 +158,5 @@
@SQ SN:R1_43_2 LN:2907
@SQ SN:R1_73_1 LN:1914
@SQ SN:R1_73_2 LN:2865
@PG ID:squigulator PN:squigulator VN:0.2.2-dirty
@PG ID:squigulator PN:squigulator VN:0.3.0-dirty
S1_1!R1_92_1!0!1637!+ 0 R1_92_1 1 255 1637M * 0 0 AAGGGGGAAGGGGGACTGGCGCGCGGCAAACCGGGGCGGCGACGAGGCCATTGACGCTCATTTCCTTCCTTTTGCCTCGGCGCCCCACCCAACCCATACACCCCCCCTCAGCGACCGCGGCTTCCGTTCTTGCAAAGGCCTATTCCAGGAGGTACCCATACCACAGCCAGTCCAGCACAACGAAACGGAGAGACCAAAGGGATGAGGAAAAGTGAGATAAATTCAGTCGACGGTTATTGAAAGAGAAAATCGAACGACAGATCCACATGATGGCTAACACTTATCCAACTCAGAAAGTGAGTGTAAAGAGGGCAACGGCGAAGGGTTAGAATGAACAACATGCCAGAAAGATTAAGAATGCGTAGAACTTGAATCGAGCGTATCTAAAGTAGAATACTTCGAAACTAGCGACTTAGGTGTTTGAGTACGCGAGTCTACAATAGAAGCAGCATGCGTTCCTGTTGGTAAGGGAGCTGGATGCTGATTCTGATGACTTTCGACTCCCCGGGTCGAGTTGTTTAAGGGAACTCGAGTACCCAGATAAGGCCAGAATGTTTAACTCTGAAGCTCTCGTCTGCTAAATAGCAATTGCGTCGCACAGTTTCGCAAATAACATATAAATCGACGGCTGGATCTCGTAGCACCAAGGTGCGATATCATCAATGCTAACCTTAATTAGCTAAGAAAGAAGTGCAACAATCTCAGAGCTTTCTTTTTAGACACCCGAACCCGAACGTTTGTTTACCCTCAGCCTCGTGCCAGGCCTGCTCATCAATACTCCTAGATTCAGACAGGAATACAACGGTGGACCGAATATCGGTTAGGCTTGTCTGATTGTTTCTTTAGACCACTAATGGTAAGAGTCCAAAAATATAAAAATAATTTCCTGTTCGGAGTGAAAAGTAAATAGAGAAAGCTATGGAATGAAGAATTGAGTGAAACAGTCGAAACTGAGAAGGAACGGGATGAAGAAGAGTGAGCAATGATGAAGCAACTGGGGACAACGAGGAATGGTTTAGTACATCTGCCCCCTCGTGAAGCCGGGACGTCACAGGAGAAGATGTTCGTGCATAAGAAGGAATATTACAATATAATGGTAGGCGGGCTAGAAGTAATAACAAATTGTGGCTAAACCTCGGGCTAACCGGAACTTCCTACGTAAAAGGAAAAGTGAACAAGGAAAAATTAATGCAAATAAATTACGGACTTGGCGCAGTAAAAAAACAGGATATCAATCCAAAGAAATCGAACCTGTCGATCGACCAGAGGGATTTGTGCCATAAGAAATAGTAGCGAGAAAAAGTACAACGGAGAAAGAGAAAGGCAAACTACCGCAGTGACCGCGAAGCAGACTAAGGCGGGGATTAACTAGCTCTGAAGATCACCATGGGCTATAGCCTCAGAAATCGGGAAACGGGGAAGAAAAGAAGAATTAGCAAGACTACCCCCAGACCAGACCGGTAATTCGGCTTCGTGGCTTTGACCGCGACATCGGTACAGGAAGGCCAGGGGGGGTGATGGGTGGGGGGGAGCGTGCACGAGCGGAAGGAAATATCTTATTAGCCACTAACGGTTGGTTATTGCTATGCCCCTTTCCGAGAAATGTTCGCGAAGTTGAGTAGCTTAGCTGGTCCAGT * si:Z:0,70084,1633,0 ss:Z:38,42,43,45,44,43,40,40,44,44,41,45,42,45,45,38,37,41,43,43,49,47,46,37,39,46,40,48,49,45,43,44,41,44,41,43,41,42,42,47,41,41,46,41,42,45,44,46,42,40,45,45,43,38,47,44,43,38,42,44,42,45,35,38,40,40,41,39,43,44,42,41,49,43,47,39,44,41,43,41,41,43,46,40,43,42,43,41,45,43,40,49,41,45,39,43,39,51,41,41,48,43,43,45,47,37,46,41,44,43,45,45,44,47,40,42,47,46,43,42,44,44,40,45,45,46,45,38,49,42,47,45,48,44,47,41,44,38,40,41,44,41,42,43,48,38,38,44,39,43,40,41,42,41,44,47,43,43,43,37,41,42,40,47,43,47,39,43,41,44,41,43,43,42,44,37,41,42,43,43,43,46,45,46,46,41,41,48,41,39,41,42,36,44,41,45,35,45,42,41,46,45,44,46,41,49,43,42,45,41,43,41,42,40,47,40,43,39,42,48,46,42,42,41,44,42,42,46,42,45,45,40,46,46,46,42,44,37,44,43,44,42,37,45,41,44,42,42,43,49,40,46,44,40,42,41,40,39,42,44,45,37,46,41,42,42,52,41,42,39,42,44,42,44,37,44,41,48,42,40,40,43,42,44,43,48,46,46,42,44,43,36,44,41,41,40,44,45,44,44,39,40,48,44,46,45,41,39,40,50,44,39,42,43,49,40,45,42,38,45,44,47,48,44,47,39,44,37,42,44,42,45,44,44,44,44,44,40,48,39,49,43,42,46,38,46,41,43,47,47,44,45,40,41,47,43,47,41,42,44,41,42,43,48,45,38,41,41,37,41,43,42,47,43,47,45,44,43,45,38,45,43,43,44,42,38,45,48,43,35,42,44,48,47,40,42,40,43,46,49,42,40,50,42,44,44,39,37,42,46,41,43,40,44,40,42,38,43,46,43,42,45,42,40,42,45,39,41,47,40,46,46,40,43,45,41,39,45,47,36,41,43,39,43,44,43,49,42,43,41,39,42,44,43,39,40,42,43,40,38,42,46,45,48,41,47,43,44,44,45,43,43,47,39,42,37,46,40,41,42,48,44,44,44,36,39,44,40,44,40,40,44,44,41,43,43,40,39,40,44,44,41,42,46,51,43,42,39,37,45,45,46,41,44,48,45,45,48,43,42,46,46,47,45,43,40,41,40,43,36,37,42,45,41,46,44,37,45,40,44,46,49,45,44,36,42,39,44,45,39,43,44,43,45,48,41,46,41,45,42,40,48,38,44,42,45,49,45,45,37,41,41,44,46,41,40,46,36,44,47,46,37,42,39,40,49,46,42,44,44,45,45,42,44,38,38,41,46,48,41,48,45,41,42,45,38,44,36,48,39,43,43,45,46,45,43,39,39,43,43,42,39,44,38,40,49,42,36,44,49,48,42,45,45,45,48,42,43,41,41,44,43,36,46,38,44,38,44,39,39,42,43,46,41,38,41,46,45,37,46,40,46,43,39,43,42,43,42,44,45,42,47,35,45,40,36,41,44,46,44,41,44,45,41,47,43,46,42,48,53,44,43,45,43,45,37,39,47,44,43,43,40,47,39,41,41,46,45,44,38,43,40,39,44,43,47,40,41,44,41,44,40,40,39,48,43,43,42,43,43,42,45,47,44,48,51,41,56,41,42,41,45,37,39,43,45,46,47,41,47,43,39,38,43,42,40,42,40,41,47,43,45,44,44,40,38,45,41,47,41,43,43,43,43,47,37,42,43,41,43,41,47,40,43,40,41,43,47,40,43,47,41,38,46,44,48,41,37,39,44,41,44,45,45,41,45,45,44,42,46,40,44,49,42,48,50,45,46,45,44,42,43,39,36,45,41,44,42,45,41,42,45,43,45,41,45,43,41,48,40,46,41,41,44,42,45,45,43,38,40,44,45,44,40,42,47,43,43,44,46,42,42,39,40,42,42,43,41,48,42,36,44,43,44,47,43,40,44,44,48,47,44,47,45,36,43,40,41,42,45,43,45,40,43,38,46,38,43,41,50,46,45,43,43,42,44,40,42,42,49,43,40,41,46,43,42,47,41,43,42,35,46,40,47,44,42,48,47,42,40,42,45,44,44,43,45,39,44,46,39,43,39,43,45,38,43,41,44,41,40,47,43,43,48,44,43,36,45,45,44,45,42,43,43,46,38,53,42,39,40,42,45,41,41,42,40,48,43,44,42,45,46,40,46,39,44,47,45,45,44,45,42,47,43,47,42,42,37,41,44,40,44,41,40,46,43,47,47,41,41,39,39,43,42,45,44,43,45,38,36,45,38,42,44,42,46,47,47,42,43,45,41,40,46,45,41,38,46,43,39,43,41,38,42,46,44,41,43,43,50,43,40,39,42,49,47,41,38,45,43,46,48,46,40,49,40,41,45,46,44,44,42,40,44,45,42,41,39,43,44,41,45,40,47,45,40,46,41,36,43,45,46,40,40,48,41,37,44,45,41,42,39,40,43,47,38,41,46,42,43,45,38,42,42,49,43,41,39,46,44,49,36,45,42,56,37,39,46,44,39,41,43,43,43,44,41,44,38,42,44,42,43,37,48,46,41,44,42,41,44,45,43,41,39,44,46,44,38,43,46,45,43,42,44,46,42,45,48,45,37,48,37,39,46,41,45,37,44,44,46,45,37,49,48,42,44,36,46,40,45,52,39,45,47,43,42,40,40,45,43,43,42,45,39,40,44,41,45,44,48,42,39,44,48,46,40,43,42,41,48,43,42,39,44,46,35,40,43,44,38,43,45,39,45,38,42,42,44,48,43,46,38,39,37,40,47,40,42,52,43,47,42,41,47,41,44,41,46,45,42,42,36,43,44,42,38,44,44,46,38,44,40,42,44,40,42,44,38,47,39,42,42,45,40,49,41,43,39,38,44,40,42,43,44,41,46,43,42,38,52,37,47,46,41,46,42,49,39,45,42,37,44,43,42,40,44,44,41,47,44,46,47,46,39,42,47,44,48,43,42,38,42,47,46,49,39,41,48,44,45,42,39,45,47,41,39,44,45,35,39,40,46,43,42,41,45,45,46,43,42,48,46,42,40,39,43,46,40,44,47,47,45,39,45,44,45,45,45,49,38,42,42,44,46,42,47,51,43,41,43,42,43,47,37,48,42,35,40,40,45,39,43,42,43,43,36,45,42,47,42,39,37,43,37,46,46,48,51,42,41,39,39,38,47,38,44,41,40,49,46,45,43,47,40,39,41,48,43,42,43,46,43,44,43,41,46,46,38,41,45,43,45,46,40,52,42,45,46,42,45,46,44,52,43,43,45,40,45,42,43,40,48,41,40,39,43,43,39,39,46,45,50,43,38,45,42,43,39,41,44,41,46,46,46,40,47,45,44,46,41,47,43,37,40,50,43,45,54,44,43,39,39,42,42,42,47,41,42,43,53,37,44,41,48,46,45,45,41,43,40,45,44,48,39,44,39,41,39,41,42,42,44,38,40,41,47,38,41,43,39,41,39,41,42,47,44,40,46,41,42,43,40,44,41,40,46,47,46,46,43,48,43,45,38,41,41,42,43,40,46,42,41,41,43,38,41,36,45,43,45,45,50,40,41,44,41,43,45,43,43,42,46,41,44,42,36,44,39,42,42,43,43,45,44,43,48,44,42,47,48,40,44,48,45,52,38,46,38,46,49,41,40,32,
6 changes: 3 additions & 3 deletions test/vupdate.sh
Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,17 @@ NEW=$2

grep "VN:$OLD" test/rna_paf.sam.exp || die "Version $OLD not found in test/rna_paf.sam.exp"
grep "VN:$OLD" test/dna_r10_paf-ref.sam.exp || die "Version $OLD not found in dna_r10_paf-ref.sam.exp"
grep "SQ_VERSION \"$OLD\"" src/sq.h || die "Version $OLD not found in src/sq.h"
grep "SQ_VERSION \"$OLD\"" src/version.h || die "Version $OLD not found in src/sq.h"
grep "VERSION=$OLD" README.md || die "Version $OLD not found in README.md"

sed -i "s/VN:$OLD/VN:$NEW/" test/rna_paf.sam.exp | grep "VN:$NEW"
sed -i "s/VN:$OLD/VN:$NEW/" test/dna_r10_paf-ref.sam.exp | grep "VN:$NEW"
sed -i "s/SQ_VERSION \"$OLD\"/SQ_VERSION \"$NEW\"/" src/sq.h | grep "SQ_VERSION \"$NEW\""
sed -i "s/SQ_VERSION \"$OLD\"/SQ_VERSION \"$NEW\"/" src/version.h | grep "SQ_VERSION \"$NEW\""
sed -i "s/VERSION=$OLD/VERSION=$NEW/" README.md | grep "VERSION=$NEW"

grep "VN:$NEW" test/rna_paf.sam.exp || die "updated version $NEW not found in test/rna_paf.sam.exp"
grep "VN:$NEW" test/dna_r10_paf-ref.sam.exp || die "updated Version $NEW not found in dna_r10_paf-ref.sam.exp"
grep "SQ_VERSION \"$NEW\"" src/sq.h || die "updated Version $NEW not found in src/sq.h"
grep "SQ_VERSION \"$NEW\"" src/version.h || die "updated Version $NEW not found in src/sq.h"
grep "VERSION=$NEW" README.md || die "updated Version $NEW not found in README.md"


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