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When I run fastq-mcf with the following command:
./fastq-mcf /home/adapters/TruSeq3-PE.fa /home/data/test.read1.fq
, it seems the program sink into dead circulation.
I use gdb to debug what happened, then navigate to this location: 271 while ( (c = getopt_long(argc, argv, "-nf0uXUVHKSRdbehp:o:O:l:s:m:t:k:x:P:q:L:C:w:F:D:",long_options,&option_inde x)) != -1) {
after all options( in my case, it means adapter file and reads file ) are gotten, value of variable "c" becomes "255", not "-1", so it can't get out of the while loop.
And I man getopt_long function, it shows that return value of this function is "int" type.
But in fastq-mcf.cpp, it defines return value as "char" type 203 char c;
I change this line, and fastq-mcf could work correctly.
The text was updated successfully, but these errors were encountered:
When I run fastq-mcf with the following command:
./fastq-mcf /home/adapters/TruSeq3-PE.fa /home/data/test.read1.fq
, it seems the program sink into dead circulation.
I use gdb to debug what happened, then navigate to this location:
271 while ( (c = getopt_long(argc, argv, "-nf0uXUVHKSRdbehp:o:O:l:s:m:t:k:x:P:q:L:C:w:F:D:",long_options,&option_inde x)) != -1) {
after all options( in my case, it means adapter file and reads file ) are gotten, value of variable "c" becomes "255", not "-1", so it can't get out of the while loop.
And I man getopt_long function, it shows that return value of this function is "int" type.
But in fastq-mcf.cpp, it defines return value as "char" type
203 char c;
I change this line, and fastq-mcf could work correctly.
The text was updated successfully, but these errors were encountered: