Your message dated Thu, 09 Apr 2020 09:50:24 +0000
with message-id <[email protected]>
and subject line Bug#956232: fixed in sumaclust 1.0.35-3
has caused the Debian Bug report #956232,
regarding sumaclust: Last sequence of input is skipped on arm64
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
956232: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956232
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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 <[email protected]>
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)
--- End Message ---
--- Begin Message ---
Source: sumaclust
Source-Version: 1.0.35-3
Done: Pierre Gruet <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sumaclust, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <[email protected]> (supplier of updated sumaclust package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 08 Apr 2020 21:49:49 +0200
Source: sumaclust
Architecture: source
Version: 1.0.35-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Pierre Gruet <[email protected]>
Closes: 956232
Changes:
sumaclust (1.0.35-3) unstable; urgency=medium
.
* Adding a patch to read ACGT-only sequences safely, fixing regression
on amd64 (Closes: #956232)
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