e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/rmskOut2.c src/hg/lib/rmskOut2.c
index fea3fc9..f7ec562 100644
--- src/hg/lib/rmskOut2.c
+++ src/hg/lib/rmskOut2.c
@@ -1,442 +1,445 @@
 /* rmskOut2.c was originally generated by the autoSql program, which also 
  * generated rmskOut2.h and rmskOut2.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "rmskOut.h"
 #include "rmskOut2.h"
 #include "obscure.h"
 #include "binRange.h"
 
 
 
 void rmskOut2StaticLoad(char **row, struct rmskOut2 *ret)
 /* Load a row from rmskOut2 table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->swScore = sqlUnsigned(row[0]);
 ret->milliDiv = sqlUnsigned(row[1]);
 ret->milliDel = sqlUnsigned(row[2]);
 ret->milliIns = sqlUnsigned(row[3]);
 ret->genoName = row[4];
 ret->genoStart = sqlUnsigned(row[5]);
 ret->genoEnd = sqlUnsigned(row[6]);
 ret->genoLeft = sqlSigned(row[7]);
 safecpy(ret->strand, sizeof(ret->strand), row[8]);
 ret->repName = row[9];
 ret->repClass = row[10];
 ret->repFamily = row[11];
 ret->repStart = sqlSigned(row[12]);
 ret->repEnd = sqlUnsigned(row[13]);
 ret->repLeft = sqlSigned(row[14]);
 ret->id = sqlUnsigned(row[15]);
 }
 
 struct rmskOut2 *rmskOut2Load(char **row)
 /* Load a rmskOut2 from row fetched with select * from rmskOut2
  * from database.  Dispose of this with rmskOut2Free(). */
 {
 struct rmskOut2 *ret;
 
 AllocVar(ret);
 ret->swScore = sqlUnsigned(row[0]);
 ret->milliDiv = sqlUnsigned(row[1]);
 ret->milliDel = sqlUnsigned(row[2]);
 ret->milliIns = sqlUnsigned(row[3]);
 ret->genoName = cloneString(row[4]);
 ret->genoStart = sqlUnsigned(row[5]);
 ret->genoEnd = sqlUnsigned(row[6]);
 ret->genoLeft = sqlSigned(row[7]);
 safecpy(ret->strand, sizeof(ret->strand), row[8]);
 ret->repName = cloneString(row[9]);
 ret->repClass = cloneString(row[10]);
 ret->repFamily = cloneString(row[11]);
 ret->repStart = sqlSigned(row[12]);
 ret->repEnd = sqlUnsigned(row[13]);
 ret->repLeft = sqlSigned(row[14]);
 ret->id = sqlUnsigned(row[15]);
 return ret;
 }
 
 struct rmskOut2 *rmskOut2LoadAll(char *fileName) 
 /* Load all rmskOut2 from a whitespace-separated file.
  * Dispose of this with rmskOut2FreeList(). */
 {
 struct rmskOut2 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileRow(lf, row))
     {
     el = rmskOut2Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rmskOut2 *rmskOut2LoadAllByChar(char *fileName, char chopper) 
 /* Load all rmskOut2 from a chopper separated file.
  * Dispose of this with rmskOut2FreeList(). */
 {
 struct rmskOut2 *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[16];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = rmskOut2Load(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct rmskOut2 *rmskOut2CommaIn(char **pS, struct rmskOut2 *ret)
 /* Create a rmskOut2 out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rmskOut2 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->swScore = sqlUnsignedComma(&s);
 ret->milliDiv = sqlUnsignedComma(&s);
 ret->milliDel = sqlUnsignedComma(&s);
 ret->milliIns = sqlUnsignedComma(&s);
 ret->genoName = sqlStringComma(&s);
 ret->genoStart = sqlUnsignedComma(&s);
 ret->genoEnd = sqlUnsignedComma(&s);
 ret->genoLeft = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->repName = sqlStringComma(&s);
 ret->repClass = sqlStringComma(&s);
 ret->repFamily = sqlStringComma(&s);
 ret->repStart = sqlSignedComma(&s);
 ret->repEnd = sqlUnsignedComma(&s);
 ret->repLeft = sqlSignedComma(&s);
 ret->id = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void rmskOut2Free(struct rmskOut2 **pEl)
 /* Free a single dynamically allocated rmskOut2 such as created
  * with rmskOut2Load(). */
 {
 struct rmskOut2 *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->genoName);
 freeMem(el->repName);
 freeMem(el->repClass);
 freeMem(el->repFamily);
 freez(pEl);
 }
 
 void rmskOut2FreeList(struct rmskOut2 **pList)
 /* Free a list of dynamically allocated rmskOut2's */
 {
 struct rmskOut2 *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     rmskOut2Free(&el);
     }
 *pList = NULL;
 }
 
 void rmskOut2Output(struct rmskOut2 *el, FILE *f, char sep, char lastSep) 
 /* Print out rmskOut2.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->swScore);
 fputc(sep,f);
 fprintf(f, "%u", el->milliDiv);
 fputc(sep,f);
 fprintf(f, "%u", el->milliDel);
 fputc(sep,f);
 fprintf(f, "%u", el->milliIns);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genoName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->genoStart);
 fputc(sep,f);
 fprintf(f, "%u", el->genoEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->genoLeft);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->repName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->repClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->repFamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->repStart);
 fputc(sep,f);
 fprintf(f, "%u", el->repEnd);
 fputc(sep,f);
 fprintf(f, "%d", el->repLeft);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 void rmskOut2OpenVerify(char *fileName, struct lineFile **retFile, boolean *retEmpty)
 /* Open repeat masker .out file and verify that it is good.
  * Set retEmpty if it has header characteristic of an empty file. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line;
 int lineSize;
 
 lineFileNeedNext(lf, &line, &lineSize);
 if (startsWith("There were no", line))
     *retEmpty = TRUE;
 line = skipLeadingSpaces(line);
 if (! ( startsWith("SW", line) || startsWith("bit", line) ) )
   errAbort("%s doesn't seem to be a RepeatMasker .out file", fileName);
 lineFileSkip(lf, 2);
 *retEmpty = FALSE;
 *retFile = lf;
 }
 
 static int negParenNum2(struct lineFile *lf, char *s)
 /* Return number where negative is shown by parenthization. */
 {
 boolean hasParen = FALSE;
 int result;
 if (*s == '(')
    {
    hasParen = TRUE;
    ++s;
    }
 if (!isdigit(s[0]) && s[0] != '-')
    errAbort("Expecting digit line %d of %s got %s\n",
         lf->lineIx, lf->fileName, s);
 result = atoi(s);
 if (hasParen)
     result = -result;
 return result;
 }
 
 static void parseClassAndFamily(char *s, char **retClass, char **retFamily)
 /* Separate repeatMasker class/family .*/
 {
 char *e = strchr(s, '/');
 if (e == NULL)
     *retClass = *retFamily = s;
 else
     {
     *e++ = 0;
     *retClass = s;
     *retFamily = e;
     }
 }
 
 struct rmskOut2 *rmskOut2ReadNext(struct lineFile *lf)
 /* Read next record from repeat masker file.  Return NULL at EOF. */
 {
 char *words[32];
 int wordCount;
 char id;
 struct rmskOut2 *ret;
 char *class, *family;
 
 if ((wordCount = lineFileChop(lf, words)) == 0)
     return NULL;
 if (wordCount != 15 )
     errAbort("Expecting 15 words - line %d of %s", lf->lineIx, lf->fileName);
 
 id = words[14][0];
 AllocVar(ret);
 ret->swScore = lineFileNeedNum(lf, words, 0);
 ret->milliDiv = round(10.0*atof(words[1]));
 ret->milliDel = round(10.0*atof(words[2]));
 ret->milliIns = round(10.0*atof(words[3]));
 ret->genoName = cloneString(words[4]);
 ret->genoStart = lineFileNeedNum(lf, words, 5)-1;
 ret->genoEnd = lineFileNeedNum(lf, words, 6);
 ret->genoLeft = -negParenNum2(lf, words[7]);
 if (sameString(words[8], "C"))
     ret->strand[0] = '-';
 else if (sameString(words[8], "+"))
     ret->strand[0] = '+';
 else
     errAbort("Unexpected strand char line %d of %s", lf->lineIx, lf->fileName);
 ret->repName = cloneString(words[9]);
 parseClassAndFamily(words[10], &class, &family);
 ret->repClass = cloneString(class);
 ret->repFamily = cloneString(family);
 if (sameString(words[8], "C"))
 {
     ret->repStart = negParenNum2(lf, words[11])-1;
     ret->repEnd = sqlSigned(words[12]);
     ret->repLeft = -negParenNum2(lf, words[13]);
 }else
 {
     ret->repLeft = -negParenNum2(lf, words[11]);
     ret->repEnd = sqlSigned(words[12]);
     ret->repStart = negParenNum2(lf, words[13])-1;
 }
 return ret;
 }
 
 struct rmskOut2 *rmskOut2Read(char *fileName)
 /* Read all records in .out file and return as list. */
 {
 struct lineFile *lf;
 boolean isEmpty;
 struct rmskOut2 *list = NULL, *el;
 
 rmskOut2OpenVerify(fileName, &lf, &isEmpty);
 if (!isEmpty)
     {
     while ((el = rmskOut2ReadNext(lf)) != NULL)
        {
        slAddHead(&list, el);
        }
     slReverse(&list);
     }
 lineFileClose(&lf);
 return list;
 }
 
 void rmskOut2WriteHead(FILE *f)
 /* Write out rmsk header lines. */
 {
 fprintf(f,
 "   SW  perc perc perc  query      position in query           matching       repeat              position in  repeat\n"
 "score  div. del. ins.  sequence    begin     end    (left)    repeat         class/family         begin  end (left)   ID\n"
 "\n");
 }
 
 static void parenNeg2(int num, char *s, size_t sSize)
 /* Write number to s, parenthesizing if negative. */
 {
 if (num <= 0)
    safef(s, sSize, "(%d)", -num);
 else
    safef(s, sSize, "%d", num);
 }
 
 void rmskOut2WriteOneOut(struct rmskOut2 *rmsk, FILE *f)
 /* Write one rmsk in .out format to file. */
 {
 char genoLeft[24], repStart[24], repLeft[24];
 char classFam[128];
 
 parenNeg2(-rmsk->genoLeft, genoLeft, sizeof(genoLeft));
 parenNeg2(rmsk->repStart+1, repStart, sizeof(repStart));
 parenNeg2(-rmsk->repLeft, repLeft, sizeof(repLeft));
 if (sameString(rmsk->repClass, rmsk->repFamily))
     safef(classFam, sizeof(classFam), "%s", rmsk->repClass);
 else
     safef(classFam, sizeof(classFam), "%s/%s",
 	  rmsk->repClass, rmsk->repFamily);
 if ( rmsk->strand[0] == '+' )
   fprintf(f, 
     "%5d %5.1f %4.1f %4.1f  %-9s %7d %7d %9s %1s  %-14s %-19s %6s %4d %6s %6d\n",
     rmsk->swScore, 0.1*rmsk->milliDiv, 0.1*rmsk->milliDel, 0.1*rmsk->milliIns, 
     rmsk->genoName, rmsk->genoStart+1, rmsk->genoEnd, genoLeft, "+", 
     rmsk->repName, classFam, repStart, rmsk->repEnd, repLeft, rmsk->id);
 else
   fprintf(f, 
     "%5d %5.1f %4.1f %4.1f  %-9s %7d %7d %9s %1s  %-14s %-19s %6s %4d %6s %6d\n",
     rmsk->swScore, 0.1*rmsk->milliDiv, 0.1*rmsk->milliDel, 0.1*rmsk->milliIns, 
     rmsk->genoName, rmsk->genoStart+1, rmsk->genoEnd, genoLeft, "C",
     rmsk->repName, classFam, repLeft, rmsk->repEnd, repStart, rmsk->id);
 
 }
 
 void rmskOut2WriteAllOut(char *fileName, struct rmskOut2 *rmskList)
 /* Write .out format file containing all in rmskList. */
 {
 FILE *f = mustOpen(fileName, "w");
 struct rmskOut2 *rmsk;
 
 rmskOut2WriteHead(f);
 for (rmsk = rmskList; rmsk != NULL; rmsk = rmsk->next)
     rmskOut2WriteOneOut(rmsk, f);
 fclose(f);
 }
 
 struct binKeeper *readRepeats2(char *chrom, char *rmskFileName, struct hash *tSizeHash)
 /* read all repeats for a chromosome of size size, returns results in binKeeper structure for fast query*/
 {
     boolean rmskRet;
     struct lineFile *rmskF = NULL;
     struct rmskOut2 *rmsk;
     struct binKeeper *bk; 
     int size;
 
     size = hashIntVal(tSizeHash, chrom);
     bk = binKeeperNew(0, size);
     assert(size > 1);
     rmskOut2OpenVerify(rmskFileName ,&rmskF , &rmskRet);
     while ((rmsk = rmskOut2ReadNext(rmskF)) != NULL)
         {
         binKeeperAdd(bk, rmsk->genoStart, rmsk->genoEnd, rmsk);
         }
     lineFileClose(&rmskF);
     return bk;
 }
 
 struct hash *readRepeatsAll2(char *sizeFileName, char *rmskDir)
 /* read all repeats for a all chromosomes getting sizes from sizeFileNmae , returns results in hash of binKeeper structure for fast query*/
 {
 boolean rmskRet;
 struct binKeeper *bk; 
 struct lineFile *rmskF = NULL;
 struct rmskOut2 *rmsk;
 struct lineFile *lf = lineFileOpen(sizeFileName, TRUE);
 struct hash *hash = newHash(0);
 char *row[2];
 char rmskFileName[256];
 
 while (lineFileRow(lf, row))
     {
     char *name = row[0];
     int size = lineFileNeedNum(lf, row, 1);
 
     if (hashLookup(hash, name) != NULL)
         warn("Duplicate %s, ignoring all but first\n", name);
     else
         {
         bk = binKeeperNew(0, size);
         assert(size > 1);
         safef(rmskFileName, sizeof(rmskFileName), "%s/%s.fa.out",rmskDir,name);
         rmskOut2OpenVerify(rmskFileName ,&rmskF , &rmskRet);
         while ((rmsk = rmskOut2ReadNext(rmskF)) != NULL)
             {
             binKeeperAdd(bk, rmsk->genoStart, rmsk->genoEnd, rmsk);
             }
         lineFileClose(&rmskF);
 	hashAdd(hash, name, bk);
         }
     }
 lineFileClose(&lf);
 return hash;
 }