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/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
index d883c94..5a235f0 100644
--- src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
+++ src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
@@ -1,121 +1,121 @@
 /* cdwMakeRepeatQa - Figure out what proportion of things align to repeats.. */
 
 /* Copyright (C) 2014 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 "options.h"
 #include "portable.h"
 #include "cdw.h"
 #include "cdwLib.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "cdwMakeRepeatQa - Figure out what proportion of things align to repeats.\n"
   "usage:\n"
   "   cdwMakeRepeatQa startFileId endFileId\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct cdwFastqFile *cdwFastqFileForFileId(struct sqlConnection *conn, long long fileId)
 /* Return cdwFastqFile associated with given file ID or NULL if none exist. */
 {
 char query[128];
 sqlSafef(query, sizeof(query), "select * from cdwFastqFile where fileId=%lld", fileId);
 return cdwFastqFileLoadByQuery(conn, query);
 }
 
 void raIntoCdwRepeatQa(char *fileName, struct sqlConnection *conn, long long fileId)
 /* Read in two column file and put it into cdwQaRepeat table. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 while (lineFileRow(lf, row))
     {
     char *repeatClass = row[0];
     double mapRatio = lineFileNeedDouble(lf, row, 1);
     char query[512];
     sqlSafef(query, sizeof(query), 
 	"insert into cdwQaRepeat (fileId,repeatClass,mapRatio) values (%lld, \"%s\", %g)",
 	fileId, repeatClass, mapRatio);
     sqlUpdate(conn, query);
     }
 lineFileClose(&lf);
 }
 
 void fastqRepeatQa(struct sqlConnection *conn, struct cdwFile *ef, struct cdwValidFile *vf)
 /* Do repeat QA if possible on fastq file. */
 {
 /* First see if total repeat content is already in our table, in which case we are done. */
 long long fileId = ef->id;
 char query[512];
 sqlSafef(query, sizeof(query), 
     "select count(*) from cdwQaRepeat where fileId=%lld and repeatClass='total'" , fileId);
 if (sqlQuickNum(conn, query) != 0)
     return;	/* We've done this already */
 
 /* Get sample file name from fastq table. */
 struct cdwFastqFile *fqf = cdwFastqFileForFileId(conn, fileId);
 if (fqf == NULL)
     errAbort("No edqFastqRecord for %s",  vf->licensePlate);
 char *fastqPath = fqf->sampleFileName;
 
 char bwaIndex[PATH_LEN];
 safef(bwaIndex, sizeof(bwaIndex), "/dev/shm/btData/repeatMasker/%s/repeatMasker.fa", 
    vf->ucscDb);
 
 char cmd[3*PATH_LEN];
 char *samName = cloneString(rTempName(cdwTempDir(), "cdwQaRepeat", ".sam"));
 //we used to use BWA here, see the discussion about BWA/bowtie in cdwLib.c
 safef(cmd, sizeof(cmd), "bowtie --mm --threads 4 %s %s -S > %s", bwaIndex, fastqPath, samName);
 mustSystem(cmd);
 
 
 char *raName = cloneString(rTempName(cdwTempDir(), "cdwQaRepeat", ".ra"));
 safef(cmd, sizeof(cmd), "edwSamRepeatAnalysis %s %s", samName, raName);
 mustSystem(cmd);
 verbose(2, "mustSystem(%s)\n", cmd);
 remove(samName);
 
 raIntoCdwRepeatQa(raName, conn, fileId);
 remove(raName);
 
 freez(&samName);
 freez(&raName);
 cdwFastqFileFree(&fqf);
 }
 
 void cdwMakeRepeatQa(int startFileId, int endFileId)
 /* cdwMakeRepeatQa - Figure out what proportion of things align to repeats.. */
 {
 struct sqlConnection *conn = cdwConnectReadWrite();
 struct cdwFile *ef, *efList = cdwFileAllIntactBetween(conn, startFileId, endFileId);
 for (ef = efList; ef != NULL; ef = ef->next)
     {
     struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
     if (vf != NULL)
 	{
 	if (sameString(vf->format, "fastq"))
 	    fastqRepeatQa(conn, ef, vf);
 	}
     }
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 cdwMakeRepeatQa(sqlUnsigned(argv[1]), sqlUnsigned(argv[2]));
 return 0;
 }