Attachment #194016 for bug #228758




# $FreeBSD$

PORTNAME=	tRNAscan-SE
PORTVERSION=	1.3.1
PORTEPOCH=	1
CATEGORIES=	biology
MASTER_SITES=	http://lowelab.ucsc.edu/software/

MAINTAINER=	ports@FreeBSD.org
COMMENT=	Improved tool for transfer RNA detection

LICENSE=	GPLv2+
DEPRECATED=	Broken for more than 6 months
EXPIRATION_DATE=	2018-06-06

USES=		perl5
MAKE_ARGS=	BINDIR="${PREFIX}/bin" \
		LIBDIR="${DATADIR}" \
		CC="${CC}" \

PORTDATA=	*
PORTDOCS=	Manual.ps

PERLMOD_DIR=	tRNAscanSE
PERLMOD_FILES=	CM.pm Constants.pm Eufind.pm GeneticCode.pm LogFile.pm \
		Options.pm ScanResult.pm Sequence.pm SS.pm Stats.pm Tscan.pm \
		Utils.pm

PLIST_DIRS+=	${SITE_PERL_REL}/${PERLMOD_DIR}
.for f in ${PERLMOD_FILES}
PLIST_FILES+=	${SITE_PERL_REL}/${PERLMOD_DIR}/${f}
.endfor

OPTIONS_DEFINE=	DOCS

post-patch:

.for f in TPCsignal Dsignal *.cm gcode.*
	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}
.endfor
	${MKDIR} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
.for f in ${PERLMOD_FILES}
	${INSTALL_DATA} ${WRKSRC}/${PERLMOD_DIR}/${f} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
.endfor
	@${MKDIR} ${STAGEDIR}${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR}


Lines 1-2 Link Here

(-)distinfo (-2 / +3 lines)
1	SHA256 (tRNAscan-SE-1.23.tar.Z) = 843caf3e258a6293300513ddca7eb7dbbd2225e5baae1e5a7bcafd509f6dd550	1	TIMESTAMP = 1528187117
2	SIZE (tRNAscan-SE-1.23.tar.Z) = 846349	2	SHA256 (tRNAscan-SE-1.3.1.tar.gz) = 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316
		3	SIZE (tRNAscan-SE-1.3.1.tar.gz) = 740960




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

Lines 7-10 Link Here

(-)pkg-descr (-1 / +1 lines)
7	post-processing, and outputting the results in one of several	7	post-processing, and outputting the results in one of several
8	formats.	8	formats.
9		9
10	WWW: http://selab.janelia.org/software.html	10	WWW: http://lowelab.ucsc.edu/tRNAscan-SE/

Return to bug 228758

Lines 2-20 Link Here

(-)Makefile (-7 / +19 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= tRNAscan-SE	4	PORTNAME= tRNAscan-SE
5	PORTVERSION= 1.23	5	PORTVERSION= 1.3.1
6	PORTREVISION= 1	6	PORTEPOCH= 1
7	CATEGORIES= biology	7	CATEGORIES= biology
8	MASTER_SITES= ftp://selab.janelia.org/pub/software/tRNAscan-SE/	8	MASTER_SITES= http://lowelab.ucsc.edu/software/
9		9
10	MAINTAINER= ports@FreeBSD.org	10	MAINTAINER= ports@FreeBSD.org
11	COMMENT= Improved tool for transfer RNA detection	11	COMMENT= Improved tool for transfer RNA detection
12		12
13	BROKEN= No public distfiles	13	LICENSE= GPLv2+
14	DEPRECATED= Broken for more than 6 months
15	EXPIRATION_DATE= 2018-06-06
16		14
17	USES= perl5 tar:Z	15	USES= perl5
18	MAKE_ARGS= BINDIR="${PREFIX}/bin" \	16	MAKE_ARGS= BINDIR="${PREFIX}/bin" \
19	LIBDIR="${DATADIR}" \	17	LIBDIR="${DATADIR}" \
20	CC="${CC}" \	18	CC="${CC}" \
Lines 25-30 Link Here
25	PORTDATA= *	23	PORTDATA= *
26	PORTDOCS= Manual.ps	24	PORTDOCS= Manual.ps
27		25
		26	PERLMOD_DIR= tRNAscanSE
		27	PERLMOD_FILES= CM.pm Constants.pm Eufind.pm GeneticCode.pm LogFile.pm \
		28	Options.pm ScanResult.pm Sequence.pm SS.pm Stats.pm Tscan.pm \
		29	Utils.pm
		30
		31	PLIST_DIRS+= ${SITE_PERL_REL}/${PERLMOD_DIR}
		32	.for f in ${PERLMOD_FILES}
		33	PLIST_FILES+= ${SITE_PERL_REL}/${PERLMOD_DIR}/${f}
		34	.endfor
		35
28	OPTIONS_DEFINE= DOCS	36	OPTIONS_DEFINE= DOCS
29		37
30	post-patch:	38	post-patch:
Lines 41-46 Link Here
41	.for f in TPCsignal Dsignal .cm gcode.	49	.for f in TPCsignal Dsignal .cm gcode.
42	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}	50	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${DATADIR}
43	.endfor	51	.endfor
		52	${MKDIR} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
		53	.for f in ${PERLMOD_FILES}
		54	${INSTALL_DATA} ${WRKSRC}/${PERLMOD_DIR}/${f} ${STAGEDIR}${SITE_PERL}/${PERLMOD_DIR}
		55	.endfor
44	@${MKDIR} ${STAGEDIR}${DOCSDIR}	56	@${MKDIR} ${STAGEDIR}${DOCSDIR}
45	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR}	57	${INSTALL_DATA} ${WRKSRC}/Manual.ps ${STAGEDIR}${DOCSDIR}
46		58

Lines 1-291 Link Here

(-)files/patch-sqio.c (-291 lines)
1	--- sqio.c.orig 2002-04-12 20:12:04 UTC
2	+++ sqio.c
3	@@ -235,7 +235,7 @@ readline(FILE f, char s)
4	}
5
6	static void
7	-getline(struct ReadSeqVars *V)
8	+get_line(struct ReadSeqVars *V)
9	{
10	readline(V->f, V->sbuffer);
11	}
12	@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
13	V->seqlen = 0;
14	if (addfirst) addseq(V->sbuffer, V);
15	do {
16	- getline(V);
17	+ get_line(V);
18	done = feof(V->f);
19	done \|= (*endTest)(V->sbuffer, &addend);
20	if (addend \|\| !done)
21	@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
22	char *sptr;
23	/* load first line of entry */
24	while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
25	- getline(V);
26	+ get_line(V);
27	if (feof(V->f)) return;
28
29	if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
30	@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
31	SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
32	}
33	do {
34	- getline(V);
35	+ get_line(V);
36	if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
37	SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
38	else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
39	@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
40	SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
41	}
42	} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
43	- getline(V); /* skip next line, coords */
44	+ get_line(V); /* skip next line, coords */
45
46	readLoop(0, endPIR, V);
47
48	@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
49	/* get next line
50	*/
51	while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
52	- getline(V);
53	+ get_line(V);
54	}
55
56
57	@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
58	char *nm;
59	/* position past ';' comments */
60	do {
61	- getline(V);
62	+ get_line(V);
63	} while (! (feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer != ';')) ));
64
65	if (!feof(V->f))
66	@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
67	}
68
69	while (!(feof(V->f) \|\| ((V->sbuffer != '\0') && (V->sbuffer == ';'))))
70	- getline(V);
71	+ get_line(V);
72	}
73
74	static int
75	@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
76	if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
77	SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
78	}
79	- getline(V);
80	+ get_line(V);
81	}
82
83	if (! feof(V->f))
84	@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
85	/* load next line
86	*/
87	while ((!feof(V->f)) && (*V->sbuffer != ';'))
88	- getline(V);
89	+ get_line(V);
90	}
91
92
93	@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
94	int in_definition;
95
96	while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
97	- getline(V);
98	+ get_line(V);
99
100	if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
101	{
102	@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
103	in_definition = FALSE;
104	while (! feof(V->f))
105	{
106	- getline(V);
107	+ get_line(V);
108	if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
109	{
110	if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
111	@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
112
113
114	while (!(feof(V->f) \|\| ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
115	- getline(V);
116	+ get_line(V);
117	/* SRE: V->s now holds "//", so sequential
118	reads are wedged: fixed Tue Jul 13 1993 */
119	while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
120	- getline(V);
121	+ get_line(V);
122	}
123
124	static int
125	@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
126	if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
127	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
128
129	- getline(V); /skip title-junk line/
130	+ get_line(V); /skip title-junk line/
131
132	readLoop(0, endNBRF, V);
133
134	while (!(feof(V->f) \|\| (V->sbuffer != 0 && V->sbuffer == '>')))
135	- getline(V);
136	+ get_line(V);
137	}
138
139
140	@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
141	} else Die("bogus GCGdata format? %s", V->sbuffer);
142
143	/* second line contains free text description */
144	- getline(V);
145	+ get_line(V);
146	SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
147
148	if (binary) {
149	@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
150	else readLoop(0, endGCGdata, V);
151
152	while (!(feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer == '>'))))
153	- getline(V);
154	+ get_line(V);
155	}
156
157	static int
158	@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
159	readLoop(0, endPearson, V);
160
161	while (!(feof(V->f) \|\| ((V->sbuffer != 0) && (V->sbuffer == '>'))))
162	- getline(V);
163	+ get_line(V);
164	}
165
166
167	@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
168
169	/* make sure we have first line */
170	while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
171	- getline(V);
172	+ get_line(V);
173
174	if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
175	{
176	@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
177	}
178
179	do {
180	- getline(V);
181	+ get_line(V);
182	if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
183	{
184	if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
185	@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
186
187	/* load next record's ID line */
188	while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
189	- getline(V);
190	+ get_line(V);
191	}
192
193
194	@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
195	{
196	char *sptr;
197
198	- getline(V); /s == "seqLen seqid string..."/
199	+ get_line(V); /s == "seqLen seqid string..."/
200
201	if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
202	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
203	@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
204	readLoop(0, endZuker, V);
205
206	while (!(feof(V->f) \| ((V->sbuffer != '\0') & (V->sbuffer == '('))))
207	- getline(V);
208	+ get_line(V);
209	}
210
211	static void
212	@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
213
214	do {
215	done = feof(V->f);
216	- getline(V);
217	+ get_line(V);
218	if (! done) addseq(V->sbuffer, V);
219	} while (!done);
220	}
221	@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
222	char *sptr;
223	int dostruc = FALSE;
224
225	- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
226	+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
227
228	if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
229	SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
230	@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
231	/CONSTCOND/
232	while (1)
233	{
234	- getline(V);
235	+ get_line(V);
236	if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
237
238	if (strncmp(V->sbuffer, "SRC ", 4) == 0)
239	@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
240	while (1)
241	{
242	/* sequence line */
243	- getline(V);
244	+ get_line(V);
245	if (feof(V->f) \|\| strncmp(V->sbuffer, "++", 2) == 0)
246	break;
247	addseq(V->sbuffer, V);
248	/* structure line */
249	if (dostruc)
250	{
251	- getline(V);
252	+ get_line(V);
253	if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
254	addstruc(V->sbuffer, V);
255	}
256	@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
257
258
259	while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
260	- getline(V);
261	+ get_line(V);
262	}
263
264
265	@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format,
266
267	/* Load the first line.
268	*/
269	- getline(dbfp);
270	+ get_line(dbfp);
271
272	return dbfp;
273	}
274	@@ -862,7 +862,7 @@ void
275	SeqfilePosition(SQFILE *sqfp, long offset)
276	{
277	fseek(sqfp->f, offset, SEEK_SET);
278	- getline(sqfp);
279	+ get_line(sqfp);
280	}
281
282
283	@@ -954,7 +954,7 @@ ReadSeq(SQFILE V, int format, char *re
284	do { /* skip leading comments on GCG file */
285	gotuw = (strstr(V->sbuffer,"..") != NULL);
286	if (gotuw) readUWGCG(V);
287	- getline(V);
288	+ get_line(V);
289	} while (! feof(V->f));
290	break;
291