Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add a test for multi-context seeds #451

Merged
merged 1 commit into from
Oct 7, 2024
Merged

Add a test for multi-context seeds #451

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 11 additions & 0 deletions tests/phix.mcs.se.paf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
SRR1377138.32 301 2 293 + NC_001422.1 5386 1434 1725 47 291 255
SRR1377138.33 301 2 297 + NC_001422.1 5386 3818 4113 47 295 255
SRR1377138.34 301 33 299 - NC_001422.1 5386 844 1110 40 266 255
SRR1377138.35 301 5 298 - NC_001422.1 5386 4041 4334 47 293 255
SRR1377138.36 301 3 301 + NC_001422.1 5386 4997 5295 51 298 255
SRR1377138.37 301 2 299 - NC_001422.1 5386 794 1091 42 297 255
SRR1377138.38 301 32 284 - NC_001422.1 5386 4971 5223 42 252 255
SRR1377138.39/1 301 1 295 - NC_001422.1 5386 1791 2085 48 294 255
SRR1377138.40 301 4 293 - NC_001422.1 5386 3020 3309 44 289 255
rescuable.42 301 4 293 - NC_001422.1 5386 3020 3309 44 289 255
not.rescuable 301 4 293 - NC_001422.1 5386 3020 3309 44 289 255
5 changes: 5 additions & 0 deletions tests/run.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,4 +116,9 @@ strobealign --no-PG --eqx --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fa
diff tests/phix.se.sam multiblock.sam
rm multiblock.fastq.gz multiblock.sam

# Single-end PAF with multi-context seeds
strobealign --mcs -x tests/phix.fasta tests/phix.1.fastq | tail -n 11 > phix.mcs.se.paf
diff tests/phix.mcs.se.paf phix.mcs.se.paf
rm phix.mcs.se.paf

echo "Success"