Broken output for a long BED record by intersectBed

[hkawaji]

Hi,

I found a broken BED record is printed by intersectBed if it is very long (probably longer than 1024bytes).
Here is an example:

# envirionment
% uname -sro ; bedtools --version
Linux 3.10.0-1160.el7.x86_64 GNU/Linux
bedtools v2.30.0

# ttn.bed12 has a single BED12 formatted transcript record
% cat ttn.bed12 | wc
      1      12    3319

# the BED12 formatted record become broken as 11 columns
% intersectBed -wa -a ttn.bed12 -b ttn.bed3 | wc
      1      11    1024

I expected to have 12 column BED record output in the last command, but the output was broken. It seems to occur when a record is longer than 1024 bytes. Notably, 'bed12ToBed6' handle the record properly and I guess it might
be an issue in printing of intersectBed, rather than the fundamental difficulties of the BEDtools suite.

The full data content of this example is below. Note that this is an actual record of human gene, not artificial example.

% cat ttn.bed3
chr2    178525988       178807421

% cat ttn.bed12
chr2    178525988       178807421       ENST00000342992.10:TTN  0       -       178527011 178804642        0       312     1319,303,154,692,157,5609,594,306,576,300,306,585,303,303,300,288,594,282,306,306,297,291,306,303,2067,300,288,294,1767,306,303,300,288,297,303,588,297,17106,303,588,297,198,105,588,288,291,288,306,303,297,288,300,303,300,276,303,300,285,321,2967,294,300,282,309,303,300,282,303,303,282,151,149,315,300,297,318,300,130,33,149,309,430,191,309,300,294,285,297,300,303,363,303,300,279,306,197,106,300,300,116,187,297,288,122,178,148,152,285,115,188,303,303,270,267,125,409,279,267,267,169,98,267,124,143,127,140,267,267,267,127,140,264,267,264,127,140,276,279,402,51,90,63,90,75,81,69,111,78,108,84,78,84,84,84,84,84,84,84,84,90,78,81,297,75,69,78,96,75,75,297,84,84,84,78,84,162,78,93,75,78,207,81,84,84,84,84,78,81,114,102,84,84,81,84,84,84,81,87,78,78,63,405,48,72,84,60,27,78,210,261,268,90,184,286,93,288,291,288,288,279,279,279,288,279,282,279,282,288,288,279,279,279,288,279,282,279,282,288,288,279,279,279,288,279,282,279,282,279,288,279,279,279,282,279,288,279,279,279,282,279,288,279,279,279,282,564,279,57,189,126,285,232,166,142,261,261,261,264,261,261,264,273,267,282,1694,169,165,272,245,234,206,143,216,64,259,66,282,123,294,138,138,138,126,138,153,331,245,86,288,204,104,210,   0,1457,2285,2539,3971,4252,9993,10949,11353,12551,12957,13393,14079,15293,16275,16673,17080,17845,18212,19399,19831,20223,20611,21014,21418,23581,23997,24978,25641,27513,27925,28464,28876,30859,31264,31659,32352,33322,50540,50934,51613,51999,52622,52817,53572,53950,54333,55510,55917,56307,56951,57618,58287,58680,59083,60516,61129,61527,61910,62549,65610,65989,66390,66786,67184,67579,67972,68355,69518,71549,71919,72517,72759,73157,73565,74865,75276,75669,75893,76013,76293,77887,78719,78998,79425,81032,81412,81796,82189,82617,83219,83695,84101,85004,85383,85769,86068,86288,86784,87172,87762,88063,88477,88858,89318,89652,90490,90740,91131,91336,91790,92200,92595,93632,93999,94228,94726,95113,95486,95851,96681,98476,99284,103312,104252,104815,105045,106158,106537,106929,107198,107424,107828,108377,108734,109176,109451,109974,110409,111380,113710,114059,114552,115252,116248,118559,119931,123828,124175,124762,125254,125464,125677,125895,126107,126275,126469,133016,133183,136977,144229,145101,145982,146418,146646,147644,148325,149050,149932,151632,152136,152425,152758,153350,153610,153905,154265,155090,155387,155672,156708,157222,158010,158341,158677,158917,159264,159529,162122,162688,163064,163301,163526,163824,166027,166508,167620,167933,168610,168840,169359,169876,171132,172854,175131,175539,176051,176179,176465,178158,178521,178888,179185,180465,180873,181537,183577,184646,185073,185955,186326,186708,187096,187908,188303,188997,189504,191106,191534,191954,192333,192706,193175,193565,193994,194396,194932,195858,196270,196670,197057,197429,197867,198271,199379,199779,201101,201596,202121,202511,202902,203299,203675,204104,204516,204936,205316,205704,206077,206451,206845,207250,207625,208339,208718,209522,212093,227135,232995,238188,238538,240392,241770,242025,242684,243690,244071,244423,245222,247120,247473,247849,248218,248932,249367,251160,251431,251715,252885,253240,254011,255132,256223,256550,256817,257731,258081,259631,259859,263371,263989,264719,266083,267415,268410,268933,273498,273836,274406,276149,278563,281223,

% intersectBed -a ttn.bed12 -b ttn.bed3
chr2    178525988       178807421       ENST00000342992.10:TTN  0       -       178527011 178804642        0       312     1319,303,154,692,157,5609,594,306,576,300,306,585,303,303,300,288,594,282,306,306,297,291,306,303,2067,300,288,294,1767,306,303,300,288,297,303,588,297,17106,303,588,297,198,105,588,288,291,288,306,303,297,288,300,303,300,276,303,300,285,321,2967,294,300,282,309,303,300,282,303,303,282,151,149,315,300,297,318,300,130,33,149,309,430,191,309,300,294,285,297,300,303,363,303,300,279,306,197,106,300,300,116,187,297,288,122,178,148,152,285,115,188,303,303,270,267,125,409,279,267,267,169,98,267,124,143,127,140,267,267,267,127,140,264,267,264,127,140,276,279,402,51,90,63,90,75,81,69,111,78,108,84,78,84,84,84,84,84,84,84,84,90,78,81,297,75,69,78,96,75,75,297,84,84,84,78,84,162,78,93,75,78,207,81,84,84,84,84,78,81,114,102,84,84,81,84,84,84,81,87,78,78,63,405,48,72,84,60,27,78,210,261,268,90,184,286,93,288,291,288,288,279,279,279,288,279,282,279,282,288,288,279,279,279,288,279,282,279,282,288,288,279,279,279,288,279,282,279,282,279,288,279,27
% cat ttn.bed12 |bed12ToBed6 |wc -l
312