Comments (6)
I'm away from my code: try to change '3' to '2' (or "1" ?) in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java#L175 and recompile
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Thanks. I modified the BlastNToSnp.java based on your suggestion and recompiled. But the problem is not fixed. there is another way ?
Best
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I've added a new option -n (int)
try to run this tool with -n 0
1907242
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Dear Pierre
Thanks for your great support. the problem is not fixed yet with your improvement. I recompiled and ran the software with -n 0. but in some cases mismatches are reported as two or three like:
1:213087129-213087330(+) gi|229627866 298 1 101 298 + T A 97 T A .
1:213087129-213087330(+) gi|229628918 115 1 101 113 + C A 159 C A .
1:213087129-213087330(+) gi|229630731 7 1 101 262 - TG CT 192 CA AG ..
1:213087129-213087330(+) gi|229631360 26 1 101 200 - TGG CCT 201 CCA AGG ...
Can you fixed the problem please ?
Thanks again for your help.
Best
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No, sorry I won't fix this; this is clearly not a SNV but a di/tri nucleotide change.
You can always try to remove the lines 204-209
jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/blast/BlastNToSnp.java
Lines 204 to 209 in 1907242
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Thanks for your help. I removed the mentioned lines but the problem was not fixed. however i fixed it by my script. Thanks again for your support.
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Related Issues (20)
- BUILD FAILED HOT 17
- sam2tsv: limit output only the intersecting positions of reads HOT 2
- Does jvarkit provide official test cases? HOT 6
- Request to add a 'plot largest n contigs' for WGSCoveragePlotter HOT 1
- Error while installing -- Running Javac HOT 2
- strange biostar214299 results HOT 2
- vcf2tab HOT 2
- Randomized runs of Biostar154220.html HOT 1
- Test AssertionError HOT 2
- build failed and test failed
- Task :vcffilterjdk FAILED HOT 1
- ./gradlew mapuniprot install error HOT 3
- Is it possible to add the 'Gene' and peptide 'POSITION(S)' info corresponding to each genomic coordinate using MapUniProtFeatures HOT 5
- Task 'MapUniProtFeatures.main()' not found in root project 'jvarkit'. HOT 2
- indel calls with msa2vcf? HOT 2
- build failed,are these packages core packages or important packages and will they affect other toolkits? HOT 2
- java.lang.StackOverflowError [Biostar175929] HOT 2
- vcf2svg
- bamrenamechr [SEVERE][ConvertBamChromosomes]Illegal state mapper==null or dict-out=null HOT 5
- questions about sam2tsv output file HOT 4
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