Package: sumaclust
Version: 1.0.35-2
Severity: normal
Tags: patch upstream
Version 1.0.35-2 of sumaclust runs on arm64 but the last sequence of input
files is always skipped.
This appears to be linked to the way sequences are read in libfasta/sequence.c.
I have proposed a patch to upstream, which seems to solve the problem. I am
waiting for its opinion on it.
Best,
Pierre
From: Pierre Gruet <pgtdeb...@free.fr>
Date: Wed, 8 Apr 2020 11:18:01 +0200
Subject: Reading only-ACGT sequences safely
---
sumalibs/libfasta/sequence.c | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/sumalibs/libfasta/sequence.c b/sumalibs/libfasta/sequence.c
index 2cf3d10..db999f8 100755
--- a/sumalibs/libfasta/sequence.c
+++ b/sumalibs/libfasta/sequence.c
@@ -162,19 +162,25 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem,
int seqLen)
{
char* seqTemp;
char c;
- int32_t index = 0, seqIndex = 0, len = strlen(seq);
+ int32_t index = 1, seqIndex = 0, len = strlen(seq);
char* seqAlphabets = "acgtACGT";
int notAllATGC = 0;
+ int goOnParsing = 1;
seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
- while (index < len)
+ while (goOnParsing)
{
c = seq[index++];
if (strchr(seqAlphabets, c) != NULL)
seqTemp[seqIndex++] = tolower(c);
+ else if (c == '\n')
+ goOnParsing = 0; //End of line character terminating
the sequence has been reached.
else if (c != '\n')
notAllATGC = 1;
+
+ if (index == len)
+ goOnParsing = 0;
}
if (notAllATGC)
