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/mouseStuff/libScan/libScan.c src/hg/mouseStuff/libScan/libScan.c
index 001729a..6967c8c 100644
--- src/hg/mouseStuff/libScan/libScan.c
+++ src/hg/mouseStuff/libScan/libScan.c
@@ -1,181 +1,181 @@
 /* libScan - Scan libraries to help find g' capped ones. */
 
 /* 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 "hash.h"
 #include "cheapcgi.h"
 #include "jksql.h"
 #include "htmshell.h"
 
 
 int dotEvery = 0;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "libScan - Scan libraries to help find g' capped ones\n"
   "usage:\n"
   "   libScan database output.html\n"
   "options:\n"
   "   -dots=N - write a dot every N mrnas/ests\n"
   );
 }
 
 char *entrezScript = "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4";
 
 void printEntrezNucleotideUrl(FILE *f, char *accession)
 /* Print URL for Entrez browser on a nucleotide. */
 {
 fprintf(f, "\"%s&db=n&term=%s\"", entrezScript, accession);
 }
 
 
 void dotOut()
 /* Put out a dot every now and then if user want's to. */
 {
 static int mod = 1;
 if (dotEvery > 0)
     {
     if (--mod <= 0)
 	{
 	fputc('.', stdout);
 	fflush(stdout);
 	mod = dotEvery;
 	}
     }
 }
 
 
 struct libInfo
 /* Info on one library. */
     {
     struct libInfo *next;
     char *idString;	/* Id as a string for hashing. */
     char *name;		/* Library name. */
     char authorId[10];	/* Author ID - checked to make sure unique. */
     boolean multiAuthor;/* More than one author? */
     int mrnaCount;	/* Number of mRNAs used. */
     int estCount;	/* Number of ESTs used. */
     char sampleAcc[12];		/* Accession of one instance of library. */
     char sampleDate[12];	/* Date of sample. */
     };
 
 boolean isOrestesForm(char *name)
 /* Is lib name in format that shows it's from Orestes project? */
 {
 int i, len = strlen(name);
 if (len < 5 || len > 6)
     return FALSE;
 if (!isupper(name[0]))
     return FALSE;
 if (!isupper(name[1]))
     return FALSE;
 for (i=2; i<len; ++i)
     if (!isdigit(name[i]))
 	return FALSE;
 return TRUE;
 }
 
 int libInfoCmpEstCount(const void *va, const void *vb)
 /* Compare to sort based on query. */
 {
 const struct libInfo *a = *((struct libInfo **)va);
 const struct libInfo *b = *((struct libInfo **)vb);
 return b->estCount - a->estCount;
 }
 
 
 void libScan(char *database, char *outName)
 /* libScan - Scan libraries to help find g' capped ones. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 char query[256];
 char **row;
 struct sqlResult *sr;
 struct libInfo *libList = NULL, *lib;
 struct hash *libHash = newHash(0);
 FILE *f = mustOpen(outName, "w");
 boolean isEst;
 
 sr = sqlGetResult(conn, NOSQLINJ "select id,name from library");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(lib);
     slAddHead(&libList, lib);
     hashAddSaveName(libHash, row[0], lib, &lib->idString);
     lib->name = cloneString(row[1]);
     }
 sqlFreeResult(&sr);
 slReverse(&libList);
 printf("Got %d libraries in %s\n", slCount(libList), database);
 
 sr = sqlGetResult(conn, NOSQLINJ "select type,library,author,acc from mrna");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     dotOut();
     lib = hashMustFindVal(libHash, row[1]);
     isEst = sameString(row[0], "EST");
     if (lib->estCount + lib->mrnaCount == 0)
 	{
 	strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc));
 	strncpy(lib->authorId, row[2], sizeof(lib->authorId));
 	}
     else
 	{
 	if (isEst && lib->estCount == 0)
 	    strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc));
 	if (!sameString(lib->authorId, row[2]))
 	    {
 	    if (!lib->multiAuthor)
 		{
 		lib->multiAuthor = TRUE;
 		}
 	    }
 	}
     if (isEst)
         ++lib->estCount;
     else
         ++lib->mrnaCount;
     }
 if (dotEvery)
    printf("\n");
 sqlFreeResult(&sr);
 slSort(&libList, libInfoCmpEstCount);
 
 htmStart(f, "cDNA Libraries");
 fprintf(f, "<PRE>");
 for (lib = libList; lib != NULL; lib = lib->next)
     {
     if (lib->estCount > 50 && !isOrestesForm(lib->name))
 	{
 	char date[16];
 	sqlSafef(query, sizeof query, "select gb_date from seq where acc = '%s'", lib->sampleAcc);
 	sqlQuickQuery(conn, query, date, sizeof(date));
 	if (!startsWith("0000", date) && strcmp(date, "1999") > 0)
 	    {
 	    fprintf(f, "<A HREF=");
 	    printEntrezNucleotideUrl(f, lib->sampleAcc);
 	    fprintf(f, ">%s</A> ", lib->sampleAcc);
 	    fprintf(f, "%s %d\t%d\t%d\t%s\n", date, lib->multiAuthor, lib->mrnaCount, lib->estCount, lib->name);
 	    }
 	}
     }
 htmEnd(f);
 
 sqlDisconnect(&conn);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 dotEvery = cgiOptionalInt("dots", dotEvery);
 if (argc != 3)
     usage();
 libScan(argv[1], argv[2]);
 return 0;
 }