From usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd Tue Apr 20 10:06:22 EST 1993 Article: 2195 of bionet.software Newsgroups: bionet.software Path: usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: ReadSeq large sequence bug Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington Date: Tue, 20 Apr 1993 15:03:15 GMT There is a bug in the current release of readseq (dated 1Feb93) which causes it to abort when fed sequences larger than a certain size, at least when compiled with certain compilers. If you feed a sequence of around 5000 base pairs or larger to readseq, and it aborts (maybe with the message "Segmentation fault") then you have found the bug. Here is a temporary correction for that bug. In the file ureadseq.c, change near top: #define kStartLength 500 to: #define kStartLength 500000 /* 20Apr93 temp. bug fix */ /* set this value higher than max seq size expected */ then recompile it, and readseq will work on large sequences. (tobacco chlorop. gene acc#Z00044 with 155844 bp for example) But this isn't a definative bug fix. It looks like the memory management code for calloc/malloc/realloc is failing where it shouldn't. I will have to look at it more. -- Don -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405