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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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does Sam2Tsv only print out variants but no perfect matches? #111

Closed Huanle closed 6 years ago

Huanle commented 6 years ago

Hi Pierre,

thanks for developing sam2tsv. Just a quick question about the ouput. It seems sam2tsv only output varaints (SNP and indels) but not perfect matches. Is this correct?

Will it be possible to let it generate reads the perfectly matched to reference at a given position.

Thanks, Huanlee

lindenb commented 6 years ago

It seems sam2tsv only output varaints (SNP and indels) but not perfect matches.

no, it prints everything.

$ java -jar dist/sam2tsv.jar -A  \
    -r samtools-0.1.18/examples/toy.fa 
      samtools-0.1.18/examples/toy.sam
r001    163 ref 0   T   .   7   T   M
r001    163 ref 1   T   .   8   T   M
r001    163 ref 2   A   .   9   A   M
r001    163 ref 3   G   .   10  G   M
r001    163 ref 4   A   .   11  A   M
r001    163 ref 5   T   .   12  T   M
r001    163 ref 6   A   .   13  A   M
r001    163 ref 7   A   .   14  A   M
Huanle commented 6 years ago

@lindenb sorry. i mistaken it with the output from another program. :( thanks.