
1.0 Paired primary alignment 
1.0.1 with flag 0x1 clear (result: spot assembly not done)
1.0.2 with flag 0x2 clear (result as 1.0)

2.0 Paired primary alignment plus secondary alignment
2.0.1 with flag 0x1 clear (result: spot assembly not done)
2.0.2 with flag 0x2 clear (result as 1.0)
2.1 Paired primary alignment plus multiple secondary alignments
2.1.1 with flag 0x1 clear (result: spot assembly not done)
2.1.2 with flag 0x2 clear (result as 1.0)
2.2 Good primary alignment, no matches on the secondary
2.2.1 with flag 0x1 clear (result: spot assembly not done)
2.2.2 with flag 0x2 clear (result as 1.0)

2.3 Good primary alignment, bad position on the secondary
2.3.1 with flag 0x1 clear (result: spot assembly not done)
2.3.2 with flag 0x2 clear (result as 1.0)

3.0 Half aligned pair (one read aligned, one isn't)
3.0.1. Half aligned pair (one read aligned, one isn't), paired with flag 0x1 clear (result: spot assembly not done)
3.1. Half aligned, half poorly aligned (no matches)
3.1.1. Half aligned, half poorly aligned (no matches), paired with flag 0x1 clear (result: spot assembly not done)
3.2. Half aligned, half poorly aligned (bad position)
3.2.1. Half aligned, half poorly aligned (bad position), paired with flag 0x1 clear (result: spot assembly not done)

4.0 Unaligned pair
4.0.1 Unaligned pair, with flag 0x1 clear (result: spot assembly not done) 
4.1. Badly aligned, unaligned pair

5.0 Unaligned no pair
5.1. Badly aligned, no pair

6.0 Aligned, no pair

7.0 Aligned, no pair with secondary, no pair

=====

x.x.2 with bad flags:
- paired, aligned, 0x2 clear (not checking it; make sure we are not screwed up - ? verify)


- paired, aligned with 0x8 clear (not checking it; make sure we are not screwed up)
- 0x20 is set but mate's 0x10 not (not checking it; make sure we are not screwed up)
- a mated record with both 0x40 and 0x80 set 
- a mated record with both 0x40 and 0x80 clear
- multiple alignments for the same spot, none of which are marked secondary (0x100)
- 0x200 set (set READ_FILTER column = REJECT)
- 0x400 set (set READ_FILTER column = CRITERIA, only if set on both mates)
- both 0x200 and 0x400 set on both of reads in a pair (result: warning, only one of the flags set)

RNAME = *, flag says it's aligned

CIGAR = *, flag says aligned

CIGAR contains hard clipping (H operations)

1.* with varying spot groups

SEQ = * (SAM allows, no sense for us - error)
QUAL = * (same)

Poorly aligned: 
	- good position, no matches (result: made unaligned)
	- bad position (=beyond the end of the reference) (result: made unaligned)

Error(warning?): Primary aligned unpaired, secondary paired

TBD: colorspace tests

TBD: header tests
