Read numbers overflow

[GaryEBenson]

Problem

in file trf2proclu-ngs.c

For large datasets, the call to this program sends in a number for the -f flag (which is the startid of the reads) which is negative because it exceeds the int max value of ~2.417 billion. It may also be negative because it is never changed from the initial value of -1000000.

My understanding (Gary) is that the jump between files is usually 1 million, but this is a padding because the files only contain 50,000 reads and the padding is to avoid having the readTR numbers in one file bump into those in the next. Is this correct? Could the id of the readTR be set to a combination of the process number and the line number instead?

The error in step 1 says the startid is less than 1.

suggested change for rollover into negative numbers.
line 310
int startid = -1000000, ...
This variable has to be made long long int
long long int startid = -1000000;

remainder of the ints on this line can remain the same.

in trf2proclu-ngs.c, line 361, use atoll for reading the -f parameter value so long long int values are preserved

suggested change to eliminate large padding, set the id of the readTR to be a combination of the process number and the line number