[Breakdancer-help] something about cpp version

[hechuan y. <yan...@gm...>]

Hi Ken,

There are some problem  comes up when I use the new version of breakdancer.
The output of BreakdancerMax.pl and it's cpp version are different
especially for the solid data.Let me show you some example:
[yanghch@submit1 solid]$ awk '$9>=60' s127.solid.max.c |type.count.pl -t7
DEL 160
INV 15
ITX 4
[yanghch@submit1 solid]$ awk '$9>=60' s127.solid.max.c.cpp |type.count.pl-t7
CTX 297812
DEL 161
INS 279
INV 15
ITX 4
[yanghch@submit1 solid]$ awk '$7=="CTX"' s127.solid.max.c |head
chr1 75803842 37+23- chr2 3042777 4+5- CTX -4731 0 2 NA|2 0.02
BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
chr1 4948321 247+255- chr2 6037495 31+18- CTX -4731 0 2 NA|2 0.00
BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
chr1 14397963 27+33- chr2 6037495 31+16- CTX -4731 0 2 NA|2 0.02
BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
chr1 57157392 133+112- chr2 5016007 142+134- CTX -4731 0 2 NA|2 0.01
BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
chr1 111486422 66+43- chr2 5016007 140+134- CTX -4731 0 2 NA|2 0.01
BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
[yanghch@submit1 solid]$ awk '$7=="CTX"' s127.solid.max.c.cpp |head
chr1 75803842 37+23- chr2 3042777 4+5- CTX -4731 99 2 NA|2 0.0206186
chr1 4948321 247+255- chr2 6037495 31+18- CTX -4731 99 2 NA|2 0.00299401
chr1 14397963 27+33- chr2 6037495 31+16- CTX -4731 99 2 NA|2 0.0210526
chr1 57157392 133+112- chr2 5016007 142+134- CTX -4731 99 2 NA|2 0.00566572
chr1 111486422 66+43- chr2 5016007 140+134- CTX -4731 99 2 NA|2 0.0120482

As you can see,the score for the same sv are not the same in the output of
perl and cpp version of BreakdcerMax.And it's not only for the CTX data.

Is the perl version more reliable?

By the way,the bed format output file of cpp version have a flaw:

track name=chr10_7096079_INS_-64        description="BreakDancer chr10
7096079 INS -64" useScore=0
chrchr10        7096068 7096142 5_mnOjLYels11|B 370     -       7096068
7096142 0,0,255
chrchr10        7096009 7096083 5_mnOjLYels11|B 370     +       7096009
7096083 255,0,0
chrchr10        7096074 7096148 7_Lr9qMMiJ321|B 370     -       7096074
7096148 0,0,255
chrchr10        7096057 7096131 7_Lr9qMMiJ321|B 370     +       7096057
7096131 255,0,0

Best wishes.

-- 
Hechuan Yang
Kunming Institute of Zoology,CAS
Kunming,Yunnan
P.R.China