Can sam4weblogo output the read quality in the aligned fastq file, instead of a fasta file.

[y9c]

sam4weblogo is a powerful tool for generate msa file from bam file.

Sometime, I need to filter the msa file with phread quality of each base. Can sam4 weblogo generate a fastq file with read quality as output?

[lindenb]

I added a new option '-q' to genrate fastq format. Can you tell me if it's working ?

[y9c]

Thank you @lindenb ! It work pretty well.

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• I keep searching to find a tool for convert bam file to MSA file. Cause the name of this tool is not distinguishable, it take me nearly an hour to find this wonderful tool. Would you mind change the name into sam2fasta/sam2fastq/sam2msa or something else?

• I notice that you add '-' symbol to fill the gap in quality string of fastq file. Howerver, - is meaningful in ASCII phred score. ord("-")-33 = 12. Could you change that into !, which is zero in the form of phred score. PacBio data use this to fill nan data.

https://github.com/lindenb/jvarkit/blob/61fe1e1c8c035fafc011b5441fa68a7c7c83edba/src/main/java/com/github/lindenb/jvarkit/tools/sam4weblogo/SAM4WebLogo.java#L189

[y9c]

https://github.com/lindenb/jvarkit/pull/110