vg surject: unhygienic output for unmapped reads

[mlin]

Unmapped reads (RNAME=*) in the BAM output from vg surject seem to have an arbitrary value filled in for POS and perhaps other fields as well. These could be dirty values left over in some data structure from a previous use.

$ samtools view aln.surn.bam
C2KC2ACXX_1:6:1101:3304:0/1     6       *       11075625        0       1S99M   *       11075625
        0       TGGGTTGATGCCATGGAAAGGGGCAGTAACTTCCTGATGTTACCATGGCAACAGTAAACTAACATGGCACACTGGTGTCTAATG
GGGGAGGTGCTTCTGC    <84><84><84><88><88><88><88><88><88><88><88><88><88><8B><8B><8B><8B><8B><8B><8B>
<8B><8B><8B><88><8B><8B><84><88><84><88><8B><8B><8B><8B><8B><8B><88><88><8B><8B><8B><88><8B><88><88>
<88><88><88><84><88><8B><8B><8B><88><88><84><88><88><8B><8B><88><88><88><88><88><88><88><88><84><88>
<88><88><88><88><88><88><84><84><84><88><88><84><88><88><88><88><88><88><84><88><88>~<84><84><84>
<84><84><88><88><88>
C2KC2ACXX_1:6:1101:3573:0/1     22      *       11077961        0       100M    *       11077961
        0       AGCAGCAGTGTTTCTGAACAGCTTCAGGAAGAGCTTGCCACTTTCAGGCTCTCACAAATGGAGAGACTTCTTATTAATCTCTTT
CTCTCCACTGCAGGCA    <84><84><84><88><88><88><88><88><88><88><88><88><88><88><88><88><88><88><88><88>
<88><88><84><88><88><88><88><88><8B><8B><88><8B><88><8B><88><88><88><88><88><8B><8B>~<88><88><8B>
<88><88><88><88><88><88><88><8B><8B><8B><8B><8B><88><8B><8B>~<88><84><84><88><88><88><8B><8B><8B>
<8B><88><8B><84><88><88><88><88><88><88>~<88><88><88>~<84><88><88><84><88><84><84><84><84><84><84>
<84><84><84><84>
C2KC2ACXX_1:6:1101:3928:0/1     22      *       11030553        0       1S99M   *       11030553
        0       GGGTAGTCTGAAAGAGCTTGTTCCTCCCCGCCTCTCTCTCTCTCTTGCTCTCTCTCTTGCCATGTAACATTCAGGCTCCTCCTT
CACCTTCCAACATGGT    <84><84><84><88><88><88><88><88><88><88><88><88><88><8B>~<88><88><88><8B><88>
<8B><8B><8B><88><88><8B><8B><88><8B><8B><8B><8B><8B><88><8B><8B><8B><8B><8B><8B><8B><8B><8B><8B><88>
<8B><8B><88><8B><8B><8B><8B><8B><8B><8B><84><88><88><8B><8B><88><88><8B><88><88><88><88><88><88><88>
<84><84><88><84>riiiriyririirrr<84>iiriririyi

[ekg]

@mcshane and I think that this is "technically" fine, in that the BAM/SAM spec allows this behavior. However, it is true that it is confusing and may cause problems downstream if tools don't first check if the read is mapped or unmapped before handling it.

[adamnovak]

I think we just need to clear out path_pos around here:

vg/src/mapper.cpp

Lines 4446 to 4456 in 2e6be77

	} else {
	surjection = source;
	#ifdef debug
	#pragma omp critical (cerr)
	cerr << "Alignment " << source.name() << " did not align to the surjection subgraph" << endl;
	#endif
	}