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blasttosam's Issues

What BLAST-output format is required as input?

Hi,

thanks for this nice tool!
I am looking forward to using it.
Could you please specify (maybe also in the README) what BLAST output format is supposed to be the input (ASN.1, XML, etc.)?

Thank you very much.

Best,

Cedric

Error about converting .sam to .bam after BlastToSam

Hi,

I get the following error message from SAMtools-0.1.19 with the most recent version of BlastToSam when applying it to an NCBI-BLAST+-2.2.30-based alignment of two reconstructed bacterial genomes, i.e., both represented by multiple contigs.
Unfortunately, I can not share the files but the command lines used:

blastn -num_threads 12 -query query.fa -db ./target -outfmt 11 -out ./query-blastn_against-target.asn
blast_formatter -archive ./query-blastn_against-target.asn -out ./query-blastn_against-target.out -outfmt 0
java -jar BlastToSam.jar -i query-blastn_against-target.out -o query-blastn_against-target.out.sam
samtools view -bS query-blastn_against-target.out.sam > query-blastn_against-target.out.bam

Do you have any idea what might be the problem?

[samopen] SAM header is present: 29 sequences.
Line 129, sequence length 129 vs 117 from CIGAR
Parse error at line 129: CIGAR and sequence length are inconsistent
Aborted

Thank you very much for your support.

Best,

Cedric

UPDATE:
I tried SAMtools-1.2 which returns the following

[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] parse error at line 129
[main_samview] truncated file.

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