tags 552862 + patch thanks Hi, The following patch seems to fix this issue.
Please note you will need to update your 30-arb-code-patches.dpatch, (line 315, change 'getline(V);' to 'mygetline(V);') Regards, Ruben Molina
--- readseq-1.orig/ureadseq.c
+++ readseq-1/ureadseq.c
@@ -142,7 +142,7 @@
}
}
-Local void getline(struct ReadSeqVars *V)
+Local void mygetline(struct ReadSeqVars *V)
{
readline(V->f, V->s, &V->linestart);
}
@@ -237,7 +237,7 @@
if (addfirst) addseq(V->s, V);
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
V->done |= (*endTest)( &addend, &ungetend, V);
if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
@@ -268,7 +268,7 @@
while (!V->allDone) {
do {
- getline(V);
+ mygetline(V);
for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
if (*si == 0) *V->s= 0; /* chop line to empty */
} while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
@@ -294,13 +294,13 @@
{ /* ? only 1 seq/file ? */
while (!V->allDone) {
- getline(V);
+ mygetline(V);
if (strstr(V->s,"; DNA sequence ") == V->s)
strcpy(V->seqid, (V->s)+16);
else
strcpy(V->seqid, (V->s)+1);
while ((!feof(V->f)) && (*V->s == ';')) {
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
else readLoop(0, true, endStrider, V);
@@ -320,16 +320,16 @@
while (!V->allDone) {
while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) )
- getline(V);
+ mygetline(V);
strcpy(V->seqid, (V->s)+16);
while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
- getline(V);
+ mygetline(V);
readLoop(0, false, endPIR, V);
if (!V->allDone) {
while (! (feof(V->f) || ((*V->s != 0)
&& (strstr( V->s,"ENTRY") == V->s))))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -354,13 +354,13 @@
while (!V->allDone) {
strcpy(V->seqid, (V->s)+12);
while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
- getline(V);
+ mygetline(V);
readLoop(0, false, endGB, V);
if (!V->allDone) {
while (! (feof(V->f) || ((*V->s != 0)
&& (strstr( V->s,"LOCUS") == V->s))))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -426,11 +426,11 @@
{
while (!V->allDone) {
strcpy(V->seqid, (V->s)+4);
- getline(V); /*skip title-junk line*/
+ mygetline(V); /*skip title-junk line*/
readLoop(0, false, endNBRF, V);
if (!V->allDone) {
while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -452,7 +452,7 @@
readLoop(0, false, endPearson, V);
if (!V->allDone) {
while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -472,14 +472,14 @@
while (!V->allDone) {
strcpy(V->seqid, (V->s)+5);
do {
- getline(V);
+ mygetline(V);
} while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s)));
readLoop(0, false, endEMBL, V);
if (!V->allDone) {
while (!(feof(V->f) |
((*V->s != '\0') & (strstr(V->s,"ID ") == V->s))))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -499,13 +499,13 @@
/*! 1st string is Zuker's Fortran format */
while (!V->allDone) {
- getline(V); /*s == "seqLen seqid string..."*/
+ mygetline(V); /*s == "seqLen seqid string..."*/
strcpy(V->seqid, (V->s)+6);
readLoop(0, false, endZuker, V);
if (!V->allDone) {
while (!(feof(V->f) |
((*V->s != '\0') & (*V->s == '('))))
- getline(V);
+ mygetline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -588,7 +588,7 @@
do {
addseq(V->s, V);
V->done = feof(V->f);
- getline(V);
+ mygetline(V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
V->allDone = true;
@@ -614,7 +614,7 @@
else if (si = strstr(V->seqid,"..")) *si = 0;
do {
V->done = feof(V->f);
- getline(V);
+ mygetline(V);
if (!V->done) addseq((V->s), V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
@@ -633,7 +633,7 @@
if (V->addit) V->seqlen = 0;
rewind(V->f); V->nseq= 0;
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -716,7 +716,7 @@
if (V->addit) V->seqlen = 0;
rewind(V->f); V->nseq= 0;
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -787,7 +787,7 @@
domatch= (V->matchchar > 0);
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -868,7 +868,7 @@
/* rewind(V->f); V->nseq= 0; << do in caller !*/
indata= true; /* call here after we find "matrix" */
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -953,7 +953,7 @@
/* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */
do {
- getline(V);
+ mygetline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -1006,7 +1006,7 @@
while (isdigit(*si)) si++;
skipwhitespace(si);
V->topseqlen= atol(si);
- getline(V);
+ mygetline(V);
while (!V->allDone) {
V->seqlencount= 0;
strncpy(V->seqid, (V->s), 10);
@@ -1037,10 +1037,10 @@
V->err = eFileNotFound;
else {
- for (l = skiplines_; l > 0; l--) getline( V);
+ for (l = skiplines_; l > 0; l--) mygetline( V);
do {
- getline( V);
+ mygetline( V);
for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
} while ((l == 0) && !feof(V->f));
@@ -1067,7 +1067,7 @@
char *cp;
/* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
while (!done) {
- getline( V);
+ mygetline( V);
tolowerstr( V->s);
if (strstr( V->s, "matrix")) done= true;
if (strstr( V->s, "interleav")) interleaved= true;
@@ -1099,7 +1099,7 @@
break;
case kFitch :
- strcpy(V->seqid, V->s); getline(V);
+ strcpy(V->seqid, V->s); mygetline(V);
readFitch(V);
break;
@@ -1107,7 +1107,7 @@
do {
gotuw = (strstr(V->s,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ mygetline(V);
} while (!(feof(V->f) || V->allDone));
break;
}
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