fefdc562bc014756f3c22f53dce16126ada37b56
hiram
  Wed Sep 8 11:09:33 2021 -0700
update bad blocks message to read as documentation refs #28131

diff --git src/hg/lib/bedDetail.c src/hg/lib/bedDetail.c
index d1d7da0..c40434f 100644
--- src/hg/lib/bedDetail.c
+++ src/hg/lib/bedDetail.c
@@ -1,434 +1,430 @@
 /* bedDetail.c was originally generated by the autoSql program, which also
  * generated bedDetail.h and bedDetail.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 "basicBed.h"
 #include "bedDetail.h"
 
 
 struct bedDetail *bedDetailLoad(char **row)
 /* Load a bedDetail from row fetched with select * from bedDetail
  * from database.  Dispose of this with bedDetailFree(). */
 {
 struct bedDetail *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(row[9]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 {
 int sizeOne;
 sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->id = cloneString(row[12]);
 ret->description = cloneString(row[13]);
 return ret;
 }
 
 struct bedDetail *bedDetailLoadAll(char *fileName)
 /* Load all bedDetail from a whitespace-separated file.
  * Dispose of this with bedDetailFreeList(). */
 {
 struct bedDetail *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = bedDetailLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bedDetail *bedDetailLoadAllByChar(char *fileName, char chopper)
 /* Load all bedDetail from a chopper separated file.
  * Dispose of this with bedDetailFreeList(). */
 {
 struct bedDetail *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bedDetailLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bedDetail *bedDetailCommaIn(char **pS, struct bedDetail *ret)
 /* Create a bedDetail out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new bedDetail */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->id = sqlStringComma(&s);
 ret->description = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void bedDetailFree(struct bedDetail **pEl)
 /* Free a single dynamically allocated bedDetail such as created
  * with bedDetailLoad(). */
 {
 struct bedDetail *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->id);
 freeMem(el->description);
 freez(pEl);
 }
 
 void bedDetailFreeList(struct bedDetail **pList)
 /* Free a list of dynamically allocated bedDetail's */
 {
 struct bedDetail *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bedDetailFree(&el);
     }
 *pList = NULL;
 }
 
 void bedDetailOutput(struct bedDetail *el, FILE *f, char sep, char lastSep, int size)
 /* Print out bedDetail.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (size > 6)
     {
     fprintf(f, "%u", el->score);
     fputc(sep,f);
     }
 if (size > 7)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->strand);
     if (sep == ',') fputc('"',f);
     fputc(sep,f);
     }
 if (size > 8)
     {
     fprintf(f, "%u", el->thickStart);
     fputc(sep,f);
     }
 if (size > 9)
     {
     fprintf(f, "%u", el->thickEnd);
     fputc(sep,f);
     }
 if (size > 10)
     {
     fprintf(f, "%u", el->reserved);
     fputc(sep,f);
     }
 if (size > 11)
     {
     fprintf(f, "%d", el->blockCount);
     fputc(sep,f);
     }
 if (size > 12)
     {
     int i;
     if (sep == ',') fputc('{',f);
     for (i=0; i<el->blockCount; ++i)
         {
         fprintf(f, "%d", el->blockSizes[i]);
         fputc(',', f);
         }
     if (sep == ',') fputc('}',f);
     fputc(sep,f);
     }
 if (size > 13)
     {
     int i;
     if (sep == ',') fputc('{',f);
     for (i=0; i<el->blockCount; ++i)
         {
         fprintf(f, "%d", el->chromStarts[i]);
         fputc(',', f);
         }
     if (sep == ',') fputc('}',f);
     fputc(sep,f);
     }
 /* last 2 should always be present */
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *bedDetailAutoSqlString =
 "table bedDetail\n"
 "\"Browser extensible data, with extended fields for detail page\"\n"
 "   (\n"
 "   string chrom;      \"Reference sequence chromosome or scaffold\"\n"
 "   uint   chromStart; \"Start position in chromosome\"\n"
 "   uint   chromEnd;   \"End position in chromosome\"\n"
 "   string name;       \"Short Name of item\"\n"
 "   uint   score;      \"Score from 0-1000\"\n"
 "   char[1] strand;    \"+ or -\"\n"
 "   uint thickStart;   \"Start of where display should be thick (start codon)\"\n"
 "   uint thickEnd;     \"End of where display should be thick (stop codon)\"\n"
 "   uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n"
 "   int blockCount;    \"Number of blocks\"\n"
 "   int[blockCount] blockSizes; \"Comma separated list of block sizes\"\n"
 "   int[blockCount] chromStarts; \"Start positions relative to chromStart\"\n"
 "   string id;         \"ID to bed used in URL to link back\"\n"
 "   lstring description; \"Long description of item for the details page\"\n"
 "   )\n"
 ;
 
 struct asObject *bedDetailAsObj()
 // Return asObject describing fields of bedDetail
 {
 return asParseText(bedDetailAutoSqlString);
 }
 
 struct bedDetail *bedDetailLoadWithGaps(char **row, int size)
 /* Load a bedDetail from row split from a file or from database,
    may have parts of BED not included.  Dispose of this with bedDetailFree().
    Size is total number of fields
 */
 {
 struct bedDetail *ret;
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 if (size > 6 && row[4] != NULL)
     ret->score = sqlUnsigned(row[4]);
 if (size > 7 && row[5] != NULL)
     safecpy(ret->strand, sizeof(ret->strand), row[5]);
 if (size > 8 && row[6] != NULL)
     ret->thickStart = sqlUnsigned(row[6]);
 if (size > 9 && row[7] != NULL)
     ret->thickEnd = sqlUnsigned(row[7]);
 if (size > 10 && row[8] != NULL)
     {
     char *comma = strchr(row[8], ',');
     if (comma)
         ret->reserved = bedParseRgb(row[8]);
     else
         ret->reserved = 0;
     }
 if (size > 11 && row[9] != NULL)
     ret->blockCount = sqlSigned(row[9]);
 if (size > 12 && row[10] != NULL)
     {
     int sizeOne;
     sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
     assert(sizeOne == ret->blockCount);
     }
 if (size > 13 && row[11] != NULL)
     {
     int sizeOne;
     sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
     assert(sizeOne == ret->blockCount);
     }
 /* these 2 should not be null, but always last 2 */
 ret->id = cloneString(row[size-2]);
 ret->description = cloneString(row[size-1]);
 return ret;
 }
 
 struct bedDetail *bedDetailLineFileLoad (char **row, int size, struct lineFile *lf)
 /* load from linefile line, with error checking */
 {
 struct bedDetail *item;
 int count; /* block count */
 int wordCount = size - 2; /* bed part of row */
 AllocVar(item);
 item->chrom = cloneString(row[0]);
 item->chromStart = lineFileNeedNum(lf, row, 1);
 item->chromEnd = lineFileNeedNum(lf, row, 2);
 if (item->chromEnd < 1)
     lineFileAbort(lf, "chromEnd less than 1 (%d)", item->chromEnd);
 if (item->chromEnd < item->chromStart)
     lineFileAbort(lf, "chromStart after chromEnd (%d > %d)",
         item->chromStart, item->chromEnd);
 if (wordCount > 3)
      item->name = cloneString(row[3]);
 if (wordCount > 4)
      item->score = lineFileNeedNum(lf, row, 4);
 if (wordCount > 5)
      {
      strncpy(item->strand, row[5], sizeof(item->strand));
      if (item->strand[0] != '+' && item->strand[0] != '-' && item->strand[0] != '.')
           lineFileAbort(lf, "Expecting + or - in strand");
      }
 if (wordCount > 6)
      item->thickStart = lineFileNeedNum(lf, row, 6);
 else
      item->thickStart = item->chromStart;
 if (wordCount > 7)
      {
      item->thickEnd = lineFileNeedNum(lf, row, 7);
      if (item->thickEnd < item->thickStart)
          lineFileAbort(lf, "thickStart after thickEnd");
      if ((item->thickStart != 0) &&
          ((item->thickStart < item->chromStart) ||
           (item->thickStart > item->chromEnd)))
          lineFileAbort(lf,
              "thickStart out of range (chromStart to chromEnd, or 0 if no CDS)");
      if ((item->thickEnd != 0) &&
          ((item->thickEnd < item->chromStart) ||
           (item->thickEnd > item->chromEnd)))
          lineFileAbort(lf,
              "thickEnd out of range for %s:%d-%d, thick:%d-%d (chromStart to chromEnd, or 0 if no CDS)",
                        item->name, item->chromStart, item->chromEnd,
                        item->thickStart, item->thickEnd);
      }
 else
      item->thickEnd = item->chromEnd;
 if (wordCount > 8)
     {
     char *comma;
     /*  Allow comma separated list of rgb values here   */
     comma = strchr(row[8], ',');
     if (comma)
         {
         int rgb = bedParseRgb(row[8]);
         if (rgb < 0)
             lineFileAbort(lf,
                 "Expecting 3 comma separated numbers for r,g,b bed item color.");
         else
             item->reserved = rgb;
         }
     else
         item->reserved = lineFileNeedNum(lf, row, 8);
     }
 if (wordCount > 9)
     item->blockCount = lineFileNeedNum(lf, row, 9);
 if (wordCount > 10)
     {
     sqlSignedDynamicArray(row[10], &item->blockSizes, &count);
     if (count != item->blockCount)
         lineFileAbort(lf,  "expecting %d elements in array", item->blockCount);
     }
 if (wordCount > 11)
     {
     int i;
     sqlSignedDynamicArray(row[11], &item->chromStarts, &count);
     if (count != item->blockCount)
         lineFileAbort(lf, "expecting %d elements in array", item->blockCount);
     // tell the user if they appear to be using absolute starts rather than
     // relative... easy to forget!  Also check block order, coord ranges...
     for (i=0;  i < item->blockCount;  i++)
         {
         if (item->chromStarts[i]+item->chromStart >= item->chromEnd)
             {
             if (item->chromStarts[i] >= item->chromStart)
                 lineFileAbort(lf,
                     "BED chromStarts offsets must be relative to chromStart, "
                     "not absolute.  Try subtracting chromStart from each offset "
                     "in chromStarts.");
             else
                 lineFileAbort(lf,
                     "BED chromStarts[i]+chromStart must be less than chromEnd.");
             }
         }
     if (item->chromStarts[0] != 0)
         lineFileAbort(lf,
             "BED blocks must span chromStart to chromEnd.  "
             "BED chromStarts[0] must be 0 (==%d) so that (chromStart + "
             "chromStarts[0]) equals chromStart.", item->chromStarts[0]);
     i = item->blockCount-1;
     if ((item->chromStart + item->chromStarts[i] + item->blockSizes[i]) !=
         item->chromEnd)
-        {
-        lineFileAbort(lf,
-            "BED blocks must span chromStart to chromEnd.  (chromStart + "
-            "chromStarts[last] + blockSizes[last]) must equal chromEnd.");
-        }
+	lineFileAbort(lf, BAD_BLOCKS);
     }
     /* these 2 should not be null (maybe empty string), but always last 2 */
     item->id = cloneString(row[size-2]);
     item->description = cloneString(row[size-1]);
 return item;
 }