secondary alignment flag

[adthrasher]

Hello, and apologies if this duplicates another issue. I searched but didn't see anything.

When running bowtie in a mode to output multiple alignments, I was surprised to see that additional alignments were not given the secondary alignment flag.

When running the following command

bowtie --chunkmbs=256 -l 51 -p 1 -k 2 -m 2 -X 600 --fr -S bowtie_index/GRCh37.p13.genome.fa-index -1 test.r1.fq -2 test.r2.fq

I get the expected 2 alignments. However, I was expecting the second pair of alignment records to have the secondary flag.

A00637:141:HFYKGDRXX:2:2269:27389:25661 99      chr1    953546  255     51M     =       953784  289     GGTGCTGATTGGTGTATTTACAATCCCTGAGCTAGACATAAAGGTTCTCCA     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF     XA:i:0  MD:Z:51 NM:i:0  XM:i:2
A00637:141:HFYKGDRXX:2:2269:27389:25661 147     chr1    953784  255     51M     =       953546  -289    GGAGGGGGTGGGAGGCTCAGGCATGGTGGGCTGCAGGTCCCCAGCTCTTCC     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF     XA:i:1  MD:Z:48G2       NM:i:1       XM:i:2
A00637:141:HFYKGDRXX:2:2269:27389:25661 99      chr1    953423  255     51M     =       953784  412     GGTGCTGATTGGTGTATTTACAATCCCTGAGCTAGACATAAAGGTTCTCCA     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF     XA:i:2  MD:Z:0A4C45     NM:i:2       XM:i:2
A00637:141:HFYKGDRXX:2:2269:27389:25661 147     chr1    953784  255     51M     =       953423  -412    GGAGGGGGTGGGAGGCTCAGGCATGGTGGGCTGCAGGTCCCCAGCTCTTCC     FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF     XA:i:1  MD:Z:48G2       NM:i:1       XM:i:2

Is there an option to enable flagging that I have missed? Thanks!