-f does not work if used with -split in v2.29

[dominik-handler]

Hi,
I came across a very strange bug. It seems that starting with v2.29 -f does not function properly anymore if used in conjunction with option -split.
read-file

cat b.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0

cat x.bed
X       0       20      B1      0       +

cat y.bed
X       0       20      B1      0       +
X       0       20      B2      0       +

cat z.bed
X       0       20      B1      0       +
X       0       20      B2      0       +
X       0       20      B1      0       +

v.2.28

./bedtools.2-28.simg intersect -wao -split -f 0.61 -a b.bed -b x.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0
./bedtools.2-28.simg intersect -wao -split -f 0.61 -a b.bed -b y.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0
./bedtools.2-28.simg intersect -wao -split -f 0.61 -a b.bed -b z.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0

v.2.29

./bedtools.2-29.simg intersect -wao -split -f 0.61 -a b.bed -b x.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0
./bedtools.2-29.simg intersect -wao -split -f 0.61 -a b.bed -b y.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B1      0       +     10
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B2      0       +     20
./bedtools.2-29.simg intersect -wao -split -f 0.61 -a b.bed -b z.bed
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B1      0       +     10
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B2      0       +     20
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B1      0       +     30

One difference I observed is the extent of overlap printed in the last column. it seems v2.29 sums this one up for all the regions in b a read in a is overlapping. If I create an example where one read can overlap the regions in y.bed then I get this:

v2.28
./bedtools.2-28.simg intersect -wao -split -f 0.61 -a a.bed -b y.bed
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B1      0       +     20
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B2      0       +     20
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0

v2.29
./bedtools.2-29.simg intersect -wao -split -f 0.61 -a a.bed -b y.bed
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B1      0       +     20
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B2      0       +     40
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B1      0       +     10
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       X       0       20      B2      0       +     20

You can see that for both reads the overlaps are summed up in v2.29 but not in v2.28.
This behavior only occurs if -split is selected.

./bedtools.2-29.simg intersect -wao  -f 0.61 -a a.bed -b y.bed
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B1      0       +     20
X       0       20      A1      1       +       0       20      255,0,0 1       20      0       X       0       20      B2      0       +     20
X       10      30      A2      1       +       0       30      255,0,0 1       20      0       .       -1      -1      .       -1      .     0

Hope this helps.

[arq5x]

There was a bug in -f -split fixed in 2.29, but the fix may have introduced another issue. I will be able to dig into this in a few days. Thanks for reporting.

[arq5x]

Thank you for reporting this bug. It has been fixed in master.