4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/utils/gtfToGenePred/gtfToGenePred.c src/hg/utils/gtfToGenePred/gtfToGenePred.c
index 4897530..92a153e 100644
--- src/hg/utils/gtfToGenePred/gtfToGenePred.c
+++ src/hg/utils/gtfToGenePred/gtfToGenePred.c
@@ -1,235 +1,235 @@
 /* gtfToGenePred - convert a GTF file to a genePred. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "gff.h"
 #include "genePred.h"
 #include "errCatch.h"
 #include "options.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gtfToGenePred - convert a GTF file to a genePred\n"
   "usage:\n"
   "   gtfToGenePred gtf genePred\n"
   "\n"
   "options:\n"
   "     -genePredExt - create a extended genePred, including frame\n"
   "      information and gene name\n"
   "     -allErrors - skip groups with errors rather than aborting.\n"
   "      Useful for getting infomation about as many errors as possible.\n"
   "     -ignoreGroupsWithoutExons - skip groups contain no exons rather than\n"
   "      generate an error.\n"
   "     -infoOut=file - write a file with information on each transcript\n"
   "     -sourcePrefix=pre - only process entries where the source name has the\n"
   "      specified prefix.  May be repeated.\n"
   "     -impliedStopAfterCds - implied stop codon in after CDS\n"
   "     -simple    - just check column validity, not hierarchy, resulting genePred may be damaged\n"
   "     -geneNameAsName2 - if specified, use gene_name for the name2 field\n"
   "      instead of gene_id.\n"
   "     -includeVersion - it gene_version and/or transcript_version attributes exist, include the version\n"
   "      in the corresponding identifiers.\n");
 }
 
 static struct optionSpec options[] = {
     {"simple", OPTION_BOOLEAN},
     {"genePredExt", OPTION_BOOLEAN},
     {"allErrors", OPTION_BOOLEAN},
     {"ignoreGroupsWithoutExons", OPTION_BOOLEAN},
     {"infoOut", OPTION_STRING},
     {"sourcePrefix", OPTION_STRING|OPTION_MULTI},
     {"impliedStopAfterCds", OPTION_BOOLEAN},
     {"geneNameAsName2", OPTION_BOOLEAN},
     {"includeVersion", OPTION_BOOLEAN},
     {NULL, 0},
 };
 boolean clGenePredExt = FALSE;  /* include frame and geneName */
 boolean clAllErrors = FALSE;    /* report as many errors as possible */
 boolean clIgnoreGroupsWithoutExons = FALSE;  /* ignore groups without exons */
 struct slName *clSourcePrefixes; /* list of source prefixes to match */
 boolean clIncludeVersion = FALSE; /* add version numbers to identifiers if available */
 unsigned clGxfOptions = 0;       /* options for converting GTF/GFF */
 boolean doSimple = FALSE;      /* only check column validity */
 int badGroupCount = 0;  /* count of inconsistent groups found */
 
 
 /* header for info file */
 static char *infoHeader = "#transId\tgeneId\tsource\tchrom\tstart\tend\tstrand\tproteinId\tgeneName\ttranscriptName\tgeneType\ttranscriptType\n";
 
 static void saveName(char **name, char *newName)
 /* if name references NULL, and newName is not NULL, update name */
 {
 if ((*name == NULL) && (newName != NULL))
     *name = newName;
 }
 static void writeInfo(FILE *infoFh, struct gffGroup *group)
 /* write a row for a GTF group from the info file */
 {
 // scan lineList for group and protein ids
 struct gffLine *ll;
 char *geneId = NULL, *proteinId = NULL, *geneName = NULL, *transcriptName = NULL, *geneVersion = NULL,
     *transcriptVersion = NULL, *proteinVersion = NULL, *geneType = NULL, *transcriptType = NULL;
 for (ll = group->lineList; ll != NULL; ll = ll->next)
     {
     saveName(&geneId, ll->geneId);
     saveName(&proteinId, ll->proteinId);
     saveName(&geneName, ll->geneName);
     saveName(&transcriptName, ll->transcriptName);
     saveName(&geneVersion, ll->geneVersion);
     saveName(&transcriptVersion, ll->transcriptVersion);
     saveName(&proteinVersion, ll->proteinVersion);
     saveName(&geneType, ll->geneType);
     saveName(&transcriptType, ll->transcriptType);
     }
 
 /* add in version numbers if requested and available */
 char geneIdToUse[1024], transcriptIdToUse[1024], proteinIdToUse[1024];
 
 if (clIncludeVersion && (geneId != NULL) && (geneVersion != NULL))
     safef(geneIdToUse, sizeof(geneIdToUse), "%s.%s", geneId, geneVersion);
 else
     safecpy(geneIdToUse, sizeof(geneIdToUse), emptyForNull(geneId));
 if (clIncludeVersion && (transcriptVersion != NULL))
     safef(transcriptIdToUse, sizeof(transcriptIdToUse), "%s.%s", group->name, transcriptVersion);
 else
     safecpy(transcriptIdToUse, sizeof(transcriptIdToUse), group->name);
 if (clIncludeVersion && (proteinId != NULL) && (proteinVersion != NULL))
     safef(proteinIdToUse, sizeof(proteinIdToUse), "%s.%s", proteinId, proteinVersion);
 else
     safecpy(proteinIdToUse, sizeof(proteinIdToUse), emptyForNull(proteinId));
 
 fprintf(infoFh, "%s\t%s\t%s\t%s\t%ld\t%ld\t%c\t%s\t%s\t%s\t%s\t%s\n",
         transcriptIdToUse, geneIdToUse, group->source,
         group->seq, group->start, group->end, group->strand,
         proteinIdToUse, emptyForNull(geneName), emptyForNull(transcriptName),
         emptyForNull(geneType), emptyForNull(transcriptType));
 }
 
 static void gtfGroupToGenePred(struct gffFile *gtf, struct gffGroup *group, FILE *gpFh,
                                FILE *infoFh)
 /* convert one gtf group to a genePred */
 {
 unsigned optFields = (clGenePredExt ? genePredAllFlds : 0);
 struct errCatch *errCatch = errCatchNew();
 
 if (errCatchStart(errCatch))
     {
     struct genePred *gp = genePredFromGroupedGtf(gtf, group, group->name, optFields, clGxfOptions);
     if (gp == NULL)
         {
         if (!clIgnoreGroupsWithoutExons)
             {
             char *msg = "no exons defined for group %s, feature %s (perhaps try -ignoreGroupsWithoutExons)";
             if (clAllErrors)
                 {
                 fprintf(stderr, msg, group->name, group->lineList->feature);
                 fputc('\n', stderr);
                 badGroupCount++;
                 }
             else
                 errAbort(msg, group->name, group->lineList->feature);
             }
         }
     else
         {
         genePredTabOut(gp, gpFh);
         genePredFree(&gp);
         }
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     // drop trailing newline in caught message
     if (endsWith(errCatch->message->string, "\n"))
         dyStringResize(errCatch->message, dyStringLen(errCatch->message)-1);
     if (clAllErrors)
         {
         fprintf(stderr, "%s\n", errCatch->message->string);
         badGroupCount++;
         }
     else
         errAbort("%s", errCatch->message->string);
     }
 else
     {
     if (infoFh != NULL)
         writeInfo(infoFh, group);
     }
 errCatchFree(&errCatch); 
 }
 
 static bool sourceMatches(struct gffGroup *group)
 /* see if the source matches on on the list */
 {
 struct slName *pre = NULL;
 for (pre = clSourcePrefixes; pre != NULL; pre = pre->next)
     if (startsWith(pre->name, group->source))
         return TRUE;
 return FALSE;
 }
         
 
 static bool inclGroup(struct gffGroup *group)
 /* check if a group should be included in the output */
 {
 if (clSourcePrefixes != NULL)
     {
     if (!sourceMatches(group))
         return FALSE;
     }
 return TRUE;
 }
 
 static void gtfToGenePred(char *gtfFile, char *gpFile, char *infoFile)
 /* gtfToGenePred -  convert a GTF file to a genePred.. */
 {
 struct gffFile *gtf = gffRead(gtfFile);
 FILE *gpFh, *infoFh = NULL;
 struct gffGroup *group;
 
 if (!gtf->isGtf)
     errAbort("%s doesn't appear to be a GTF file (GFF not supported by this program)", gtfFile);
 gffGroupLines(gtf);
 gpFh = mustOpen(gpFile, "w");
 if (infoFile != NULL)
     {
     infoFh = mustOpen(infoFile, "w");
     fputs(infoHeader, infoFh);
     }
 
 if (!doSimple)
     for (group = gtf->groupList; group != NULL; group = group->next)
 	if (inclGroup(group))
 	    gtfGroupToGenePred(gtf, group, gpFh, infoFh);
 
 carefulClose(&gpFh);
 gffFileFree(&gtf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 clGenePredExt = optionExists("genePredExt");
 doSimple = optionExists("simple");
 clIgnoreGroupsWithoutExons = optionExists("ignoreGroupsWithoutExons");
 clAllErrors = optionExists("allErrors");
 clIncludeVersion = optionExists("includeVersion");
 clSourcePrefixes = optionMultiVal("sourcePrefix", NULL);
 if (optionExists("impliedStopAfterCds"))
     clGxfOptions |= genePredGxfImpliedStopAfterCds;
 if (optionExists("geneNameAsName2"))
     clGxfOptions |= genePredGxfGeneNameAsName2;
 if (optionExists("includeVersion"))
     clGxfOptions |= genePredGxfIncludeVersion;
 gtfToGenePred(argv[1], argv[2], optionVal("infoOut", NULL));
 if (badGroupCount > 0)
     errAbort("%d errors", badGroupCount);
 return 0;
 }