AlgoLab/PIntron — Issue #10: Segmentation fault during suffix-tree preprocessing
Author: yp
Created: 2011-12-16 16:25:27+00:00
State: open
Labels: bug

If PIntron is built with `STATUS=debug`, the first step of PIntron (`est-fact`) gives a segmentation fault during the suffix-tree preprocessing phase on [these sequences](https://gist.github.com/34f17cde21fddfb5e993).
Step `est-fact` correctly completes if it is compiled with `STATUS=production`.
In particular, the last messages of the log are:

````
* INFO (main ) Creating the suffix tree (src/main-est-fact.c:276)
* INFO (log_info ) log-information gst-construction-begin 1324051456 4210 239 167 81 0 2556 0 (src/util.c:220)
* INFO (log_info ) log-information gst-preprocessing-begin 1324051474 4210 239 167 81 0 2556 0 (src/util.c:220)
* DEBUG(main ) Preprocessing the GST (src/main-est-fact.c:293)
* DEBUG(preprocess_text ) Alphabet: |ACGNT| (src/aug_suffix_tree.c:112)
* DEBUG(preprocess_text ) Occurrences of A: 2086 ( 0) (src/aug_suffix_tree.c:115)
* DEBUG(preprocess_text ) Occurrences of C: 2122 ( 2086) (src/aug_suffix_tree.c:115)
* DEBUG(preprocess_text ) Occurrences of G: 1896 ( 4208) (src/aug_suffix_tree.c:115)
* DEBUG(preprocess_text ) Occurrences of N: 50001 ( 6104) (src/aug_suffix_tree.c:115)
* DEBUG(preprocess_text ) Occurrences of T: 1984 ( 56105) (src/aug_suffix_tree.c:115)
* INFO (stree_preprocess..) Starting the suffix-tree preprocessing phase with 1 strings (src/aug_suffix_tree.c:227)
Segmentation fault
````

PIntron version: `v1.2.24`
Input files: https://gist.github.com/34f17cde21fddfb5e993
Command-line:

````
./bin-debug/pintron --bin-dir=./bin-debug/ -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=issue10 --output=pintron-full-output.json --gtf=pintron-cds-annotated-isoforms.gtf --extended-gtf=pintron-all-isoforms.gtf --logfile=pintron-pipeline-log.txt --general-logfile=pintron-log.txt
````