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gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

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Problem of overflow

thecgs opened this issue · comments

commented

Hi, gpertea

I am encountering an issue where the chromosome size exceeded the C++ integer limit INT_MAX. Can I fix it? Furthermore, Stringtie suffers from the same problem.

Such as:

(base) [chenguisen@worker03 ~]$ cat test.gff
LG05    .       gene    2170260657      2170308184      .       +       .       ID=PasufLG05C27399G00002
LG05    .       mRNA    2170260657      2170308184      .       +       .       ID=PasufLG05C27399G00002.t1;Parent=PasufLG05C27399G00002
LG05    .       exon    2170260657      2170260828      .       +       .       ID=PasufLG05C27399G00002.t1.exon1;Parent=PasufLG05C27399G00002.t1
LG05    .       exon    2170307997      2170308184      .       +       .       ID=PasufLG05C27399G00002.t1.exon2;Parent=PasufLG05C27399G00002.t1
LG05    .       CDS     2170260657      2170260828      .       +       0       ID=PasufLG05C27399G00002.t1.cds;Parent=PasufLG05C27399G00002.t1
LG05    .       CDS     2170307997      2170308184      .       +       2       ID=PasufLG05C27399G00002.t1.cds;Parent=PasufLG05C27399G00002.t1

(base) [chenguisen@worker03 ~]$ gffread test.gff -T
LG05    .       transcript      -2124706639     -2124659112     .       +       .       transcript_id "PasufLG05C27399G00002.t1"; gene_id "PasufLG05C27399G00002"
LG05    .       exon    -2124706639     -2124706468     .       +       .       transcript_id "PasufLG05C27399G00002.t1"; gene_id "PasufLG05C27399G00002";
LG05    .       exon    -2124659299     -2124659112     .       +       .       transcript_id "PasufLG05C27399G00002.t1"; gene_id "PasufLG05C27399G00002";
LG05    .       CDS     -2124706639     -2124706468     .       +       0       transcript_id "PasufLG05C27399G00002.t1"; gene_id "PasufLG05C27399G00002";
LG05    .       CDS     -2124659299     -2124659112     .       +       2       transcript_id "PasufLG05C27399G00002.t1"; gene_id "PasufLG05C27399G00002";