44ccfacbe3a3d4b300f80d48651c77837a4b571e
galt
  Tue Apr 26 11:12:02 2022 -0700
SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix.

diff --git src/hg/altSplice/lib/pfamDat.c src/hg/altSplice/lib/pfamDat.c
index ff2b077..68084f5 100644
--- src/hg/altSplice/lib/pfamDat.c
+++ src/hg/altSplice/lib/pfamDat.c
@@ -1,656 +1,656 @@
 /* pfamDat.c was originally generated by the autoSql program, which also 
  * generated pfamDat.h and pfamDat.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "pfamDat.h"
 
 
 void pfamHitStaticLoad(char **row, struct pfamHit *ret)
 /* Load a row from pfamHit table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->model = row[0];
 ret->descript = row[1];
 ret->score = atof(row[2]);
 ret->eval = atof(row[3]);
 ret->numTimesHit = sqlUnsigned(row[4]);
 }
 
 struct pfamHit *pfamHitLoad(char **row)
 /* Load a pfamHit from row fetched with select * from pfamHit
  * from database.  Dispose of this with pfamHitFree(). */
 {
 struct pfamHit *ret;
 
 AllocVar(ret);
 ret->model = cloneString(row[0]);
 ret->descript = cloneString(row[1]);
 ret->score = atof(row[2]);
 ret->eval = atof(row[3]);
 ret->numTimesHit = sqlUnsigned(row[4]);
 return ret;
 }
 
 struct pfamHit *pfamHitLoadAll(char *fileName) 
 /* Load all pfamHit from a whitespace-separated file.
  * Dispose of this with pfamHitFreeList(). */
 {
 struct pfamHit *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileRow(lf, row))
     {
     el = pfamHitLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamHit *pfamHitLoadAllByChar(char *fileName, char chopper) 
 /* Load all pfamHit from a chopper separated file.
  * Dispose of this with pfamHitFreeList(). */
 {
 struct pfamHit *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[5];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = pfamHitLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamHit *pfamHitCommaIn(char **pS, struct pfamHit *ret)
 /* Create a pfamHit out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new pfamHit */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->model = sqlStringComma(&s);
 ret->descript = sqlStringComma(&s);
 ret->score = sqlDoubleComma(&s);
 ret->eval = sqlDoubleComma(&s);
 ret->numTimesHit = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void pfamHitFree(struct pfamHit **pEl)
 /* Free a single dynamically allocated pfamHit such as created
  * with pfamHitLoad(). */
 {
 struct pfamHit *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->model);
 freeMem(el->descript);
 freez(pEl);
 }
 
 void pfamHitFreeList(struct pfamHit **pList)
 /* Free a list of dynamically allocated pfamHit's */
 {
 struct pfamHit *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pfamHitFree(&el);
     }
 *pList = NULL;
 }
 
 void pfamHitOutput(struct pfamHit *el, FILE *f, char sep, char lastSep) 
 /* Print out pfamHit.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->model);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->descript);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->score);
 fputc(sep,f);
 fprintf(f, "%f", el->eval);
 fputc(sep,f);
 fprintf(f, "%u", el->numTimesHit);
 fputc(lastSep,f);
 }
 
 void pfamDHitStaticLoad(char **row, struct pfamDHit *ret)
 /* Load a row from pfamDHit table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->model = row[0];
 ret->domain = sqlSigned(row[1]);
 ret->numDomain = sqlSigned(row[2]);
 ret->seqStart = sqlUnsigned(row[3]);
 ret->seqEnd = sqlUnsigned(row[4]);
 ret->seqRep = row[5];
 ret->hmmStart = sqlUnsigned(row[6]);
 ret->hmmEnd = sqlUnsigned(row[7]);
 ret->hmmRep = row[8];
 ret->dScore = atof(row[9]);
 ret->dEval = atof(row[10]);
 ret->alignment = row[11];
 }
 
 struct pfamDHit *pfamDHitLoad(char **row)
 /* Load a pfamDHit from row fetched with select * from pfamDHit
  * from database.  Dispose of this with pfamDHitFree(). */
 {
 struct pfamDHit *ret;
 
 AllocVar(ret);
 ret->model = cloneString(row[0]);
 ret->domain = sqlSigned(row[1]);
 ret->numDomain = sqlSigned(row[2]);
 ret->seqStart = sqlUnsigned(row[3]);
 ret->seqEnd = sqlUnsigned(row[4]);
 ret->seqRep = cloneString(row[5]);
 ret->hmmStart = sqlUnsigned(row[6]);
 ret->hmmEnd = sqlUnsigned(row[7]);
 ret->hmmRep = cloneString(row[8]);
 ret->dScore = atof(row[9]);
 ret->dEval = atof(row[10]);
 ret->alignment = cloneString(row[11]);
 return ret;
 }
 
 struct pfamDHit *pfamDHitLoadAll(char *fileName) 
 /* Load all pfamDHit from a whitespace-separated file.
  * Dispose of this with pfamDHitFreeList(). */
 {
 struct pfamDHit *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = pfamDHitLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamDHit *pfamDHitLoadAllByChar(char *fileName, char chopper) 
 /* Load all pfamDHit from a chopper separated file.
  * Dispose of this with pfamDHitFreeList(). */
 {
 struct pfamDHit *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = pfamDHitLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamDHit *pfamDHitCommaIn(char **pS, struct pfamDHit *ret)
 /* Create a pfamDHit out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new pfamDHit */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->model = sqlStringComma(&s);
 ret->domain = sqlSignedComma(&s);
 ret->numDomain = sqlSignedComma(&s);
 ret->seqStart = sqlUnsignedComma(&s);
 ret->seqEnd = sqlUnsignedComma(&s);
 ret->seqRep = sqlStringComma(&s);
 ret->hmmStart = sqlUnsignedComma(&s);
 ret->hmmEnd = sqlUnsignedComma(&s);
 ret->hmmRep = sqlStringComma(&s);
 ret->dScore = sqlDoubleComma(&s);
 ret->dEval = sqlDoubleComma(&s);
 ret->alignment = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void pfamDHitFree(struct pfamDHit **pEl)
 /* Free a single dynamically allocated pfamDHit such as created
  * with pfamDHitLoad(). */
 {
 struct pfamDHit *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->model);
 freeMem(el->seqRep);
 freeMem(el->hmmRep);
 freeMem(el->alignment);
 freez(pEl);
 }
 
 void pfamDHitFreeList(struct pfamDHit **pList)
 /* Free a list of dynamically allocated pfamDHit's */
 {
 struct pfamDHit *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pfamDHitFree(&el);
     }
 *pList = NULL;
 }
 
 void pfamDHitOutput(struct pfamDHit *el, FILE *f, char sep, char lastSep) 
 /* Print out pfamDHit.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->model);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->domain);
 fputc(sep,f);
 fprintf(f, "%d", el->numDomain);
 fputc(sep,f);
 fprintf(f, "%u", el->seqStart);
 fputc(sep,f);
 fprintf(f, "%u", el->seqEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seqRep);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->hmmStart);
 fputc(sep,f);
 fprintf(f, "%u", el->hmmEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hmmRep);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%f", el->dScore);
 fputc(sep,f);
 fprintf(f, "%f", el->dEval);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->alignment);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 struct pfamDat *pfamDatLoad(char **row)
 /* Load a pfamDat from row fetched with select * from pfamDat
  * from database.  Dispose of this with pfamDatFree(). */
 {
 struct pfamDat *ret;
 char *s;
 
 AllocVar(ret);
 ret->seqName = cloneString(row[0]);
 ret->sequence = cloneString(row[1]);
 s = row[2];
 if(s != NULL && differentString(s, ""))
    ret->pfamHitList = pfamHitCommaIn(&s, NULL);
 s = row[3];
 if(s != NULL && differentString(s, ""))
    ret->pfamDHitList = pfamDHitCommaIn(&s, NULL);
 return ret;
 }
 
 struct pfamDat *pfamDatLoadAll(char *fileName) 
 /* Load all pfamDat from a whitespace-separated file.
  * Dispose of this with pfamDatFreeList(). */
 {
 struct pfamDat *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = pfamDatLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamDat *pfamDatLoadAllByChar(char *fileName, char chopper) 
 /* Load all pfamDat from a chopper separated file.
  * Dispose of this with pfamDatFreeList(). */
 {
 struct pfamDat *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = pfamDatLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct pfamDat *pfamDatCommaIn(char **pS, struct pfamDat *ret)
 /* Create a pfamDat out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new pfamDat */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->seqName = sqlStringComma(&s);
 ret->sequence = sqlStringComma(&s);
 s = sqlEatChar(s, '{');
 if(s[0] != '}')    slSafeAddHead(&ret->pfamHitList, pfamHitCommaIn(&s,NULL));
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 if(s[0] != '}')    slSafeAddHead(&ret->pfamDHitList, pfamDHitCommaIn(&s,NULL));
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void pfamDatFree(struct pfamDat **pEl)
 /* Free a single dynamically allocated pfamDat such as created
  * with pfamDatLoad(). */
 {
 struct pfamDat *el;
 
 if ((el = *pEl) == NULL) return;
 freez(&el->header);
 freeMem(el->seqName);
 freeMem(el->sequence);
 pfamHitFreeList(&el->pfamHitList);
 pfamDHitFreeList(&el->pfamDHitList);
 freez(pEl);
 }
 
 void pfamDatFreeList(struct pfamDat **pList)
 /* Free a list of dynamically allocated pfamDat's */
 {
 struct pfamDat *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     pfamDatFree(&el);
     }
 *pList = NULL;
 }
 
 void pfamDatOutput(struct pfamDat *el, FILE *f, char sep, char lastSep) 
 /* Print out pfamDat.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seqName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sequence);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 if(el->pfamHitList != NULL)    pfamHitCommaOut(el->pfamHitList,f);
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 if(el->pfamDHitList != NULL)    pfamDHitCommaOut(el->pfamDHitList,f);
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 static void addHitTabs(char *line, int *offsets, int offsetCount)
 /* Add a tab at the correct offsets for a pfam file. */
 {
 int i;
 int tmpOffset = 0;
 int maxFuzzy =2;
 for(i=0; i < offsetCount; i++)
     {
     maxFuzzy = 2;
     tmpOffset = offsets[i];
     /* Sometimes we have to back up a space or two. */
     while(line[tmpOffset] != ' ' && maxFuzzy >= 0)
 	{
 	tmpOffset--;
 	maxFuzzy--;
 	}
     if(line[tmpOffset] != ' ')
 	errAbort("pfamDat::addHitTabs() - Found a '%c' where expecting a ' ' at position %d in line %s",
 		 line[tmpOffset], tmpOffset, line);
     line[tmpOffset] = '\t';
     }
 }
 
 void determineOffsets(char *line, int **offsets, int *offsetCount)
 /* Take the pfam line with the underlines '-----   ------' and 
    determine their field starting positions from it. Free offsets
    with freez(). */
 {
 int numBlocks = chopByWhite(line, NULL, 0);
 int i = 0, length = strlen(line); //  int offSets[] = {15,54,62,72}; int offSets[] = {15,19,23,29,35,38,44,50,54,61};
 AllocArray(*offsets, numBlocks - 1);
 *offsetCount = 0;
 for(i = 0; i < length -1; i++)
     {
     if(line[i] != '-' && line[i+1] == '-') 
 	{
 	if(*offsetCount > numBlocks -1)
 	    errAbort("pfamDat::determineOffsets() - Found too many offset.");
 	(*offsets)[(*offsetCount)++] = i;
 	}
     }
 }
 
 struct pfamDat *pfamDatFromPfamFile(char *fileName)
 /* Parse a hmmpfam generated file and return a pfamDat structure 
    containing hits. */
 {
 struct lineFile *lf = NULL;
 struct pfamDat *pfamDat = NULL;
 char *line=NULL, *mark=NULL;
 char *startToken = "Query sequence: ";
 char *pfamToken = "hmmpfam";
 char *domainToken = "Parsed for domains:";
 char *noResToken = "[no hits above thresholds]";
 char *alignmentToken = "Alignments";
 int numStrings=0;
-struct dyString *header = newDyString(512);
+struct dyString *header = dyStringNew(512);
 struct pfamHit *pfamHit = NULL;
 struct pfamDHit *pfamDHit = NULL;
-struct dyString *alignment = newDyString(1024);
+struct dyString *alignment = dyStringNew(1024);
 char *slash = NULL;
 int i;
 char **row;
 int *offsets = NULL;
 int offsetCount = 0;
 
 AllocArray(row, 15);
 
 lf = lineFileOpen(fileName, TRUE);
 /* Make sure this is a pfam file. */
 
 lineFileNextReal(lf, &line);
 if(startsWith(pfamToken, line) == FALSE)
     errAbort("pfamDat::pfamDatFromPfamFile() - %s doesn't start with %s. "
 	     "Probably not a hmmpfam generated file.", fileName, pfamToken);
 
 /* Find end of headers. */
 dyStringPrintf(header, "%s\n",line);
 while(lineFileNextReal(lf, &line))
     {
     if(startsWith(startToken, line))
 	break;
     else
 	dyStringPrintf(header, "%s\n",line);
     }
 
 /* Parse out seq name. */
 mark = line+strlen(startToken);
 AllocVar(pfamDat);
 pfamDat->seqName = cloneString(mark);
 pfamDat->sequence = cloneString("NA");
 
 /* Get the global hits. */
 while(lineFileNextReal(lf, &line))
     if(startsWith("--------",line))
 	break;
 determineOffsets(line, &offsets, &offsetCount);
 while(lineFileNextReal(lf, &line))
     {
     if(strlen(line) < 2 || strstr(line,noResToken) || startsWith(domainToken,line))
 	break;
     addHitTabs(line, offsets, offsetCount);
     numStrings = chopByChar(line, '\t', row, 15);
     for(i=0;i<numStrings;i++)
 	row[i] = trimSpaces(row[i]);
     pfamHit = pfamHitLoad(row);
     slAddHead(&pfamDat->pfamHitList, pfamHit);
     }
 slReverse(&pfamDat->pfamHitList);
 freez(&offsets);
 offsetCount = 0;
 /* Get the domain hits. */
 while(lineFileNextReal(lf, &line))
     if(startsWith("--------",line))
 	break;
 determineOffsets(line, &offsets, &offsetCount);
 while(lineFileNextReal(lf, &line))
     {
     if(strlen(line) < 2 || strstr(line,noResToken) || startsWith(alignmentToken,line))
 	break;
 //    addDHitTabs(line, offsets, offsetCount);
     /* Change the slash in the first field to a space. */
     slash = strchr(line+offsets[0], '/');
     if(slash != NULL)
 	slash[0] = ' ';
     numStrings = chopByWhite(line, row, 15);
     for(i=0;i<numStrings;i++)
 	row[i] = trimSpaces(row[i]);
     pfamDHit = pfamDHitLoad(row);
     slAddHead(&pfamDat->pfamDHitList, pfamDHit);
     }
 slReverse(&pfamDat->pfamDHitList);
 freez(&offsets);
 offsetCount = 0;
 
 /* Get the domain hits. */
 lineFileNextReal(lf, &line);
 
 for(pfamDHit = pfamDat->pfamDHitList; pfamDHit != NULL; pfamDHit=pfamDHit->next)
     {
     dyStringClear(alignment);
     dyStringPrintf(alignment, "%s", line);
     while(lineFileNextReal(lf, &line))
 	{
 	if(strstr(line, ":") || startsWith("//", line))
 	    {
 	    pfamDHit->alignment = cloneString(alignment->string);
 	    break;
 	    }
 	dyStringPrintf(alignment, "@%s", line);
 	}
     }
 lineFileClose(&lf);
 dyStringFree(&alignment);
 freez(&row);
 pfamDat->header = cloneString(header->string);
 dyStringFree(&header);
 return pfamDat;
 }
 
 void pfamDatWritePfamFile(struct pfamDat *pfamDat, char *fileName)
 /* Write out a pfam file, mimicking pfam file format enough to diff. */
 {
 
 FILE *out = mustOpen(fileName,"w");
 int nameWidth = 15, descWidth=38;
 struct pfamHit *pHit = NULL;
 struct pfamDHit *pDHit = NULL;
 
 if(pfamDat->header == NULL)
     fputs("hmmpfam - search one or more sequences against HMM database\n"
       "Freely distributed under the GNU General Public License (GPL)\n"
       "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n"
       "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\nQuery sequence: ", out);
 else
     fprintf(out, "%s\nQuery sequence: ", pfamDat->header);
 fprintf(out,"%s\n", pfamDat->seqName);
 fputs("Accession:      [none]\n"
       "Description:    [none]\n"
       "\n"
       "Scores for sequence family classification (score includes all domains):\n"
       "Model           Description                             Score    E-value  N \n"
       "--------        -----------                             -----    ------- ---\n", out);
 if(pfamDat->pfamHitList == NULL)
     fprintf(out, "	[no hits above thresholds]\n");
 else
     {
     for(pHit = pfamDat->pfamHitList; pHit != NULL; pHit = pHit->next)
 	{
 	fprintf(out, "%-*s %-*.*s %7.1f %10.2g %3d\n",
 		nameWidth, 
 		pHit->model,
 		descWidth, descWidth, pHit->descript,
 		pHit->score, pHit->eval, pHit->numTimesHit);
 	}
     }
 fputs( "Parsed for domains:\n"
       "Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value\n"
       "--------        ------- ----- -----    ----- -----      -----  -------\n",out);
 if(pfamDat->pfamDHitList == NULL)
     fprintf(out, "	[no hits above thresholds]\n");
 for(pDHit = pfamDat->pfamDHitList; pDHit != NULL; pDHit = pDHit->next)
     {
     fprintf(out, "%-*s %3d/%-3d %5d %5d %s %5d %5d %s %7.1f %8.2g\n",
 	    nameWidth, 
 	    pDHit->model,
 	    pDHit->domain, pDHit->numDomain,
 	    pDHit->seqStart, pDHit->seqEnd, 
 	    pDHit->seqRep,
 	    pDHit->hmmStart, pDHit->hmmEnd, 
 	    pDHit->hmmRep,
 	    pDHit->dScore, pDHit->dEval);
     }
 fputs("\nAlignments of top-scoring domains:\n",out);
 if(pfamDat->pfamDHitList == NULL)
     fprintf(out, "	[no hits above thresholds]\n");
 for(pDHit = pfamDat->pfamDHitList; pDHit != NULL; pDHit = pDHit->next)
     {
     subChar(pDHit->alignment, '@', '\n');
     fprintf(out,"%s\n\n", pDHit->alignment);
     }
 fprintf(out, "//");
 carefulClose(&out);
 }