file_tag must be set to generate maps

[mp15]

Hi

file_tag

scaffHiC/src/scaffHiC.c

Line 381 in cfefbde

if(file_tag == 0)

must be set to zero to generate align.sam

scaffHiC/src/scaffHiC.c

Line 384 in cfefbde

sprintf(syscmd,"%s/bwa mem -t %d -5SPM tarseq.fastq %s %s > align.sam",bindir,n_nodes,file_read1,file_read2);

to generate your map

scaffHiC/src/scaffHiC.c

Line 712 in cfefbde

sprintf(syscmd,"%s/PretextMap -o %s < align.sam > mapview.out",bindir,mapviewhic);

otherwise because align.sam is never generated scaffHiC will error when trying to generate the map.

Martin