• Register
1 vote


I have done:

cut -f FR07937945--FR07937944_gridss.vcf.gridss_RPostProcess.bedpe

and confirmed that all of the second column (QUAL) are digits. Some are integers, but most are floats.

Since line 387 of Event.java is:

int p1 = Integer.parseInt(bits[1]);

I guess there is an issue here.

Is it that BEDPE files shouldn't have floats in the QUAL col,
or is it that our file isn't a bedpe file, or is it that this is an error in clove?

Please help me.

10 7 2
6,060 points

Please log in or register to answer this question.

1 Answer

1 vote


You can solve this thing in two formats:

BED format

As described on the UCSC Genome see  below, 
the BED format is a concise and flexible way to represent genomic features and annotations. 
The BED format description supports up to 12 columns, but only the first 3 are required for the UCSC browser, 
the Galaxy browser and for bedtools. bedtools allows one to use the “BED12” format (that is, all 12 fields listed below). 
However, only intersectBed, coverageBed, genomeCoverageBed, and bamToBed will obey the BED12 “blocks” when computing overlaps, etc., 
via the “-split” option. For all other tools, the last six columns are not used for any comparisons by the bedtools. Instead, 
they will use the entire span (start to end) of the BED12 entry to perform any relevant feature comparisons. 
The last six columns will be reported in the output of all comparisons.

BEDPE format

We chose to define a new format because the existing “blocked” BED format (a.k.a. BED12)
 does not allow inter-chromosomal feature definitions. In addition, BED12 only has one strand field, 
which is insufficient for paired-end sequence alignments, especially when studying structural variation

GFF format  
Genome file format
SAM/BAM format
VCF format

Hope this may solve your problem.

11 6 4
34,950 points

Related questions

0 votes
1 answer 13 views
0 votes
1 answer 204 views
Problem: I have fundamental knowledge on java , json and gson. I have below method: public static Object parseStringToObject(String json) {     String Object = json;     Gson gson = new Gson();     Object objects = gson.fromJson(object, Object. ... strange error message: "com.google.gson.JsonSyntaxException: java.lang.IllegalStateException: Expected BEGIN_OBJECT but was STRING at line 1 column 1"
asked Aug 4, 2020 Raphael Pacheco 4.9k points
0 votes
1 answer 37 views
I am new to this. I just want to know how to do that?
asked Nov 6, 2020 TeamScript 13.5k points
0 votes
1 answer 18 views
Problem: To understand this example, you should have the knowledge of the following Java programming topics: Java Variables and (Primitive) Data Types Java while and do...while Loop Java for Loop
asked Nov 6, 2020 Mashhoodch 9.1k points
0 votes
1 answer 37 views
I was working on that. I just want to know how to do that?
asked Nov 5, 2020 TeamScript 13.5k points
2 votes
1 answer 14 views
Problem: Hello all, I am a secondary school level student and recently started learning Java programming out my curiosity. I have got a textbook on Java programming. I just completed the chapter of for-loop and continue solving the exercises of this chapter. I have got weird a ... you guys. But, yeah it is important to know for me. Thanks for being nice to me. I must recognize your help. Thanks.
asked Apr 12, 2020 Gavin 15.3k points
0 votes
1 answer 6 views
Problem: java.lang.illegalstateexception: expected begin_object but was string at line 1 column 1 path $
asked 2 days ago Muneeb Saadii 2.4k points
0 votes
1 answer 5 views
the problem I do not know the reason and I want a solution with an example in order to understand the topic and can address the problem. Thank you
asked Feb 5 ahmedadel9090 2.6k points
0 votes
1 answer 29 views
Problem: Hi there! I have started learning java just recently and I found a problem in a programming exercise in which I have to find the second largest number in a given array using programming. I know how to find the largest number, but I am facing difficulty ... number. Can anybody here help me solve the problem? Also, provide the example program so that I can understand it better. Thanks!
asked Jan 2 Code Learner 5.8k points
0 votes
1 answer 46 views
Problem: We can locate the second biggest number in an exhibit in java by arranging the cluster and restoring the second biggest number. We should see the full guide to locate the second biggest number in java exhibit.
asked Nov 5, 2020 Mashhoodch 9.1k points