#a list of references to use
R:name=c1,value=NC_011752.1
R:name=c2,value=NC_000001.10
R:name=c3,value=NC_000002.11
R:name=c4,value=NC_000003.11

#a pair of 2 prim alignments
P:name=A1,ref=c1,pos=1000,qual=!
P:name=A1,ref=c1,pos=1200,cigar=10MAAAA10M,noqual=y
L:name=A1

# 100 alignment pairs
A:name=AA,ref=c2
A:name=AA,ref=c2
C:name=AA

#B:AA,0,c2,20,100

#a different pair of 2 prim alignments
P:name=A2,flags=0x0200,ref=c3,pos=1200,cigar=10MAAAA3D10M
P:name=A2,flags=0x0400,ref=c3,pos=1400,cigar=ACGTACGT
L:name=A2
#and with a sec. alignment
S:name=A2,ref=c4,pos=1500,cigar=45M
L:name=A2,id0=0,id1=2

#a different pair of 2 prim alignments
P:name=A3,flags=0x0200,ref=c3,pos=1200,cigar=10MAAAA3D10M,mapq=2
P:name=A3,ref=c4,pos=1200,cigar=ACGTACGT
L:name=A3

#a single unaligned read
U:name=U1,seq=ACCGT