---
Reference genome, AF086833
SRR Run, SRR1972739
---
Total alignments, 20740
Unmapped, 5461
echo Mapped, 15279
Proper pair, 15216
Reads on forward strand, 8936
Reads on reverse strand, 6343
Reads mapped but mate unmapped, 11
Reads in file 1 where mate is on reverse strand, 2947
Reads in file 2 on the forward strand where mate in file 1 is on reverse strand, 2975
----
Flags
Command: samtools flags MREVERSE,READ1
0x60	96	MREVERSE,READ1

Command: samtools flags 96
0x60	96	MREVERSE,READ1

--- Work strategy ---
Suppose you need: supplementary alignments from file 1
on the forward strand where the mate is on the reverse
First find flags for each attribute:

0x10	16	REVERSE
0x800	2048	SUPPLEMENTARY
0x20	32	MREVERSE
0x40	64	READ1

# Perform the filtering (long form):
samtools view -c -F 16 -f 2048 -f 32 -f 64 results.bam
7

# Perform the filtering (short form, all flags combined into one):
samtools view -c -F 16 -f 2144 results.bam
7