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Divide-by-zero from `DBstats -mdust` #13

Closed pb-cdunn closed 8 years ago

pb-cdunn commented 8 years ago 
#0  Realloc (p=0x612090, size=0, mesg=0x0) at DB.c:57
#1  0x00000000004049ab in Trim_DB (db=0x7fffffffe300) at DB.c:621
#2  0x0000000000401834 in main (argc=2, argv=0x7fffffffe668) at DBstats.c:112
thegenemyers commented 8 years ago

My root now contains a version that now incorporates your fix and suggested add ons:

DBdust div-by-zero with empty tracks:

 I fixed this and incidentally also now guard against div-by-0 if

the DB happens to be empty. I retained the code to compute the average and standard deviation of the length of a masks' intervals, and completed the intention by printing these stats out for each mask :-)

Realloc does behave wierdly with size=0. Rather than ignore the call (and leave potentially a very big block still allocated, I patched it by setting size=1 if it comes in <= 0.

I show the bad arg as per you edits, and I added stdio.h to QV.h

I did not add a .gitignore to the repository: I have one locally, and I think everyone should, but generally I find everybody does it there own way in their development area, so I don't want pulls to potentially wipe out someone's customized .gitignore.
(My .gitignore ignores .gitignore :-) )

Cheers,
     Gene

On 3/3/16, 6:16 AM, Christopher Dunn wrote:

  • When I use DBdust with a high enough |-t| that there is no "dust" found, |DBstats -mdust| crashes on calculating the average dust length. |ave| and |dev| are not even used there, so I've removed them.
  • After that change, there is an /Out of memory/ reported for |realloc()| on a zero-size array, via |Trim_DB()|. (I don't know why that happens only for the case of empty dust tracks.)

|#0 Realloc (p=0x612090, size=0, mesg=0x0) at DB.c:57

1 0x00000000004049ab in Trim_DB (db=0x7fffffffe300) at DB.c:621

2 0x0000000000401834 in main (argc=2, argv=0x7fffffffe668) at DBstats.c:112

|

  • I've also added || in a file that technically needs it. (That is useful for a Nim http://nim-lang.org/ wrapper I am writing for _DAZZDB.)
  • Finally, I've added a proper |.gitignore|, to make |git add .| work better.
    You can view, comment on, or merge this pull request online at:

https://github.com/thegenemyers/DAZZ_DB/pull/13

    Commit Summary

— Reply to this email directly or view it on GitHub https://github.com/thegenemyers/DAZZ_DB/pull/13.

pb-cdunn commented 8 years ago

Thanks, Dr. Myers! That helps.

Some warnings:

DBdump.c:581:12: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized]
       iter = init_file_iterator(input);
            ^
DBdump.c:702:5: warning: 'pts' may be used uninitialized in this function [-Wmaybe-uninitialized]
     free(pts);
     ^
DBdump.c:593:16: warning: 'reps' may be used uninitialized in this function [-Wmaybe-uninitialized]
           { if (c >= reps)
                ^
DBdump.c:681:40: warning: 'qv_val' may be used uninitialized in this function [-Wmaybe-uninitialized]
                   putchar(qv_map[qv_val[k++]]);
                                        ^
DBdump.c:678:19: warning: 'qv_idx' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 e = qv_idx[i+1];

As for .gitignore, I have this in my ${HOME}/.config/git/ignore:

*.d
*.o
*.a

But I cannot ignore the executables in a generic way. So a minimal .gitignore for this repo would be:

Catrack
DAM2fasta
DB2fasta
DB2quiva
DBdump
DBdust
DBrm
DBshow
DBsplit
DBstats
fasta2DAM
fasta2DB
quiva2DB
simulator

You do not need to have a .gitignore locally that is not committed. For local ignore-overrides, you may use .git/info/exclude. For more details on gitignore files:

git help gitignore
thegenemyers commented 8 years ago

I have modified DBdump.c to avoid the warnings.

I'll check into the .gitignore options, thanks for the pointer.

-- Gene

On 3/5/16, 5:52 PM, Christopher Dunn wrote:

Thanks! That helps.

Some warnings:

DBdump.c:581:12: warning: 'input' may be used uninitialized in this function [-Wmaybe-uninitialized] iter = init_file_iterator(input); ^ DBdump.c:702:5: warning: 'pts' may be used uninitialized in this function [-Wmaybe-uninitialized] free(pts); ^ DBdump.c:593:16: warning: 'reps' may be used uninitialized in this function [-Wmaybe-uninitialized] { if (c >= reps) ^ DBdump.c:681:40: warning: 'qv_val' may be used uninitialized in this function [-Wmaybe-uninitialized] putchar(qv_map[qv_val[k++]]); ^ DBdump.c:678:19: warning: 'qv_idx' may be used uninitialized in this function [-Wmaybe-uninitialized] e = qv_idx[i+1];

As for |.gitignore|, I have this in my |${HOME}/.config/git/ignore|:

.d .o *.a

But I cannot ignore the executables in a generic way. So a minimal |.gitignore| for this repo would be:

Catrack DAM2fasta DB2fasta DB2quiva DBdump DBdust DBrm DBshow DBsplit DBstats fasta2DAM fasta2DB quiva2DB simulator

You do not need to have a |.gitignore| locally that is not committed. For local ignore-overrides, you may use |.git/info/exclude|. For more details on gitignore files https://git-scm.com/docs/gitignore:

git help gitignore

— Reply to this email directly or view it on GitHub https://github.com/thegenemyers/DAZZ_DB/pull/13#issuecomment-192685511.

pb-cdunn commented 8 years ago

Danke schön!