about FLAG fields in the SAM format

[tinkering]

HI, friends,

I am confused by the FLAG field in the SAM format.

according to the SAM format instruction,
http://samtools.sourceforge.net/SAM1.pdf

it mentioned that it is a bitwise FLAG, Int, [0-2^16-1]:
FLAG: bitwise FLAG. Each bit is explained in the following table:
-----------------------
Bit Description
0x1 template having multiple segments in sequencing
0x2 each segment properly aligned according to the aligner
0x4 segment unmapped
0x8 next segment in the template unmapped
0x10 SEQ being reverse complemented
0x20 SEQ of the next segment in the template being reversed
0x40 the rst segment in the template
0x80 the last segment in the template
0x100 secondary alignment
0x200 not passing quality controls
0x400 PCR or optical duplicate
---------------------------
Question:
1.How to convert the Int in the FLAG field to Bit-described above?
and vice verse
e.g. how to know 16 means with type of Bit in the above table?
2. If I want to know which strand (+/-) the segment mapped?
which Int of FLAG stands for + & - strands, respectively?

Many thanks!

[kcchan]

I think you will find this link very helpful: http://picard.sourceforge.net/explain-flags.html

[swbarnes2]

Question:
1.How to convert the Int in the FLAG field to Bit-described above?
and vice verse

Your sam file will have the number in decimal form. The description you are reading from has them in hexidecimal. Just convert.

Yes, it's weird that it's called a binary flag, but it's represented in decimal in the file, and represented in hex in the .sam file descriptor.

So 16 = 0x10, means "mapped in reverse".