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Prevent collision with getline(3)
This commit is contained in:
Baptiste Daroussin
parent
7250841fe9
commit
b8902fca51
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=415128
291
biology/tRNAscan-SE/files/patch-sqio.c
Normal file
291
biology/tRNAscan-SE/files/patch-sqio.c
Normal file
@ -0,0 +1,291 @@
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--- sqio.c.orig 2002-04-12 20:12:04 UTC
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+++ sqio.c
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@@ -235,7 +235,7 @@ readline(FILE *f, char *s)
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}
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static void
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-getline(struct ReadSeqVars *V)
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+get_line(struct ReadSeqVars *V)
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{
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readline(V->f, V->sbuffer);
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}
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@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
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V->seqlen = 0;
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if (addfirst) addseq(V->sbuffer, V);
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do {
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- getline(V);
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+ get_line(V);
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done = feof(V->f);
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done |= (*endTest)(V->sbuffer, &addend);
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if (addend || !done)
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@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
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char *sptr;
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/* load first line of entry */
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) return;
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if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
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@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
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}
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do {
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- getline(V);
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+ get_line(V);
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if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
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SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
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else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
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@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
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}
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} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
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- getline(V); /* skip next line, coords */
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+ get_line(V); /* skip next line, coords */
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readLoop(0, endPIR, V);
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@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
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/* get next line
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*/
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while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
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char *nm;
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/* position past ';' comments */
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do {
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- getline(V);
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+ get_line(V);
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} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
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if (!feof(V->f))
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@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
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}
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while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
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if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
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}
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- getline(V);
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+ get_line(V);
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}
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if (! feof(V->f))
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@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
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/* load next line
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*/
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while ((!feof(V->f)) && (*V->sbuffer != ';'))
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- getline(V);
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+ get_line(V);
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}
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@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
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int in_definition;
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while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
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- getline(V);
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+ get_line(V);
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if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
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{
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@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
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in_definition = FALSE;
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while (! feof(V->f))
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{
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- getline(V);
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+ get_line(V);
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if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
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@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
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while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
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- getline(V);
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+ get_line(V);
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/* SRE: V->s now holds "//", so sequential
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reads are wedged: fixed Tue Jul 13 1993 */
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while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
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if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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- getline(V); /*skip title-junk line*/
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+ get_line(V); /*skip title-junk line*/
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readLoop(0, endNBRF, V);
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while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
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- getline(V);
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+ get_line(V);
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}
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@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
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} else Die("bogus GCGdata format? %s", V->sbuffer);
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/* second line contains free text description */
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- getline(V);
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+ get_line(V);
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SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
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if (binary) {
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@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
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else readLoop(0, endGCGdata, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ get_line(V);
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}
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static int
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@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
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readLoop(0, endPearson, V);
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while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
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- getline(V);
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+ get_line(V);
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}
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@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
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/* make sure we have first line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ get_line(V);
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if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
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{
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@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
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}
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do {
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- getline(V);
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+ get_line(V);
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if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
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{
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if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
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@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
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/* load next record's ID line */
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while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
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{
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char *sptr;
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- getline(V); /*s == "seqLen seqid string..."*/
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+ get_line(V); /*s == "seqLen seqid string..."*/
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if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
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readLoop(0, endZuker, V);
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while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
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- getline(V);
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+ get_line(V);
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}
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static void
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@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
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do {
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done = feof(V->f);
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- getline(V);
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+ get_line(V);
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if (! done) addseq(V->sbuffer, V);
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} while (!done);
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}
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@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
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char *sptr;
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int dostruc = FALSE;
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- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
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+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
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if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
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SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
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@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
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/*CONSTCOND*/
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while (1)
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{
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
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if (strncmp(V->sbuffer, "SRC ", 4) == 0)
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@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
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while (1)
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{
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/* sequence line */
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- getline(V);
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+ get_line(V);
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if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
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break;
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addseq(V->sbuffer, V);
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/* structure line */
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if (dostruc)
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{
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- getline(V);
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+ get_line(V);
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if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
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addstruc(V->sbuffer, V);
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}
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@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
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while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
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- getline(V);
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+ get_line(V);
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}
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@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format,
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/* Load the first line.
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*/
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- getline(dbfp);
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+ get_line(dbfp);
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return dbfp;
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}
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@@ -862,7 +862,7 @@ void
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SeqfilePosition(SQFILE *sqfp, long offset)
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{
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fseek(sqfp->f, offset, SEEK_SET);
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- getline(sqfp);
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+ get_line(sqfp);
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}
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@@ -954,7 +954,7 @@ ReadSeq(SQFILE *V, int format, char **re
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do { /* skip leading comments on GCG file */
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gotuw = (strstr(V->sbuffer,"..") != NULL);
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if (gotuw) readUWGCG(V);
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- getline(V);
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+ get_line(V);
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} while (! feof(V->f));
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break;
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