undesired 'mm_map_frag rechain' in sam file
TDDB-limagrain opened this issue · comments
Dear Blend development team,
I was interesting in testing BLEND for short read mapping. The mapping of paired-end Illumina reads against a tomato genome work perfectly but the output sam file contained 252 lines with "mm_map_frag rechain" after the PG line:
@SQ SN:17-PSC-SL_TK14181.1.0_Chr11 LN:53848686
@SQ SN:17-PSC-SL_TK14181.1.0_Chr12 LN:68218429
@RG ID:var1 SM:var1 LB:Solution PL:illumina PU:none
@PG ID:blend PN:blend VN:1.0 CL:blend -ax sr -t 4 -R @RG\tID:var1\tSM:var1\tLB:Solution\tPL:illumina\tPU:none slycopersicum.fasta.ind reads_1.fastq.gz reads_2.fastq.gz
mm_map_frag rechain
mm_map_frag rechain
...
These lines seem to be problematic for further processing with samtools:
samtools flagstat tmp.sam
[W::sam_read1_sam] Parse error at line 16
samtools flagstat: error reading from "tmp.sam"
Best regards,
Thomas
Dear @TDDB-limagrain,
Thanks for this catch. The line producing this output was originally added for debugging purposes and was inadvertently left in the code.
I have now removed this line and fixed the issue in commit 6f19e37. Could you please pull the latest version of the code, compile, and try again?
Thanks,
Can
Hi Can,
it is fixed now! thanks a lot.
Best regards,
Thomas