#45 inconsistent behavior of gcphrap

open
nobody
None
5
2005-08-11
2005-08-11
Anonymous
No

Seems that gcphrap will nicely ignore exp files that
don't exist in the current directory, BUT only if it's
not the first entry in the file of file names. If for
example I create a fofn with only two entries, the
first refers to a file that does not exist, the second
does exist, I get the below output:

G129P61678FG12.T0.exp <--- does NOT exist in filesystem
G129P61678G12T10gR.T2.exp <----- does exist in filesystem

Total space allocated: 0.504 Mbytes; currently free:
0.499 Mbytes in 2 blocks
max_subclone_size: 5000Reading query file into memory
...G129P61678FG12.T0.exp: couldn't read file
Done
Total space allocated: 0.504 Mbytes; currently free:
0.360 Mbytes in 2 blocks
Complementing ... Done
Total space allocated: 0.504 Mbytes; currently free:
0.374 Mbytes in 3 blocks
Allocating align_entries ...
FATAL ERROR: qual_area size

Now if I swap the entries in the fofn and run it again
I get the following output (exiting with a successful 0)

Printing contigs ...
G129P61678G12.x//G129P61678G12T10gR.T2.exp 900
(350) Done
Total space allocated: 5.040 Mbytes; currently free:
4.512 Mbytes in 5 blocks
Total # segment blocks: 0, size: 0.000 Mbytes
Writing contigs ... (as experiment files) Done
Total space allocated: 5.040 Mbytes; currently free:
4.512 Mbytes in 6 blocks
Mapping reads by name ...

Subclone/read contig links and consistency checks (* =
inconsistency; Contig 0 = singlets)
Max subclone size: 5000

Size histogram for consistent forward-reverse pairs
(*** = inconsistent pairs)
*** 0

Done
Total space allocated: 5.040 Mbytes; currently free:
4.512 Mbytes in 6 blocks
Consistent opp sense links (* = not used in chain, **
= multiple non-zero):Checking pairs ... Done
Total space allocated: 5.040 Mbytes; currently free:
4.512 Mbytes in 6 blocks
Total space allocated: 5.040 Mbytes; currently free:
4.512 Mbytes in 6 blocks
Total # pairs: 0, size: 0.000 Mbytes
Total # segment blocks: 0, size: 0.000 Mbytes
Total # diffs: 0, in 0 lists, size: 0.000 Mbytes
Total # tags: 0, size: 0.000 Mbytes

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