SEQ and QUAL have different lengths

[sdwfrost]

I can't process the SAM output from ssw_test with samtools as the sequence length and quality score are different lengths:

ssw_test -m 1 -x 2 -o 4 -e 3 -f 14 -r -s -h -c ref.fas query.fastq > query.sam

followed by

samtools view -bS query.sam

gives

[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 3
[bam_flagstat_core] Truncated file? Continue anyway.

The first line of my SAM file is:

@HD	VN:1.4	SO:queryname
@SQ	SN:EU239217.1	LN:3212
NS500125:171:H5WMJAFXX:4:21605:21022:14089	16	EU239217.1	2682	5	104S14=32S	*	0	0	TTGTATTGAAAAACTCACTTAGATTTTATATTTTGTTATATTCTAAAAGTTTTATGGTTTTTCATTTTGCATTTGTGTGTATGATTCATTTTGAGTTCATTTTTGAGAAAGGTATAAAGTCTGTGCCTGGATTAATTTTTTTTTTTTTTT	/E<EE<EEEE/<EE	AS:i:14	NM:i:150	ZS:i:10

The quality string is way shorter than the sequence.

[mengyao]

Dear Simon,

I apologize for the error.

It has been fixed. Please clone and try the latest version.

Please let me know, if you find any other problem.

Many thanks,

Mengyao

On Fri, Nov 18, 2016 at 10:08 AM, Simon Frost notifications@github.com
wrote:

I can't process the SAM output from ssw_test with samtools as the
sequence length and quality score are different lengths:

ssw_test -m 1 -x 2 -o 4 -e 3 -f 14 -r -s -h -c ref.fas query.fastq >
query.sam

followed by

samtools view -bS query.sam

gives

[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 3
[bam_flagstat_core] Truncated file? Continue anyway.

The first line of my SAM file is:

@hd VN:1.4 SO:queryname
@sq SN:EU239217.1 LN:3212
NS500125:171:H5WMJAFXX:4:21605:21022:14089 16 EU239217.1 2682 5 104S14=32S * 0 0 TTGTATTGAAAAACTCACTTAGATTTTATATTTTGTTATATTCTAAAAGTTTTATGGTTTTTCATTTTGCATTTGTGTGTATGATTCATTTTGAGTTCATTTTTGAGAAAGGTATAAAGTCTGTGCCTGGATTAATTTTTTTTTTTTTTT /E<EE<EEEE/<EE AS:i:14 NM:i:150 ZS:i:10

The quality string is way shorter than the sequence.

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[sdwfrost]

Almost! It appears that the quality score is one base shorter than the sequence.

[mengyao]

I just made a update. Please have a check.

Sorry for the error.

On Sat, Nov 19, 2016 at 4:32 AM, Simon Frost notifications@github.com
wrote:

Almost! It appears that the quality score is one base shorter than the
sequence.

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