ba68274702714fed37a44f6e890f4f23c750bffc
braney
  Thu Dec 7 12:07:09 2017 -0800
fix problem I introduced causing liftOver to only output ~50 regions

diff --git src/hg/hgLiftOver/hgLiftOver.c src/hg/hgLiftOver/hgLiftOver.c
index 0f9bdf5..0b36f2d 100644
--- src/hg/hgLiftOver/hgLiftOver.c
+++ src/hg/hgLiftOver/hgLiftOver.c
@@ -7,31 +7,30 @@
 #include "hCommon.h"
 #include "jksql.h"
 #include "portable.h"
 #include "linefile.h"
 #include "dnautil.h"
 #include "fa.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "hdb.h"
 #include "hui.h"
 #include "cart.h"
 #include "web.h"
 #include "hash.h"
 #include "liftOver.h"
 #include "liftOverChain.h"
-#include "windowsToAscii.h"
 
 
 /* CGI Variables */
 #define HGLFT_USERDATA_VAR "hglft_userData"     /* typed/pasted in data */
 #define HGLFT_DATAFILE_VAR "hglft_dataFile"     /* file of data to convert */
 #define HGLFT_FROMORG_VAR "hglft_fromOrg"         /* FROM organism */
 #define HGLFT_FROMDB_VAR "hglft_fromDb"         /* FROM assembly */
 #define HGLFT_TOORG_VAR   "hglft_toOrg"           /* TO organism */
 #define HGLFT_TODB_VAR   "hglft_toDb"           /* TO assembly */
 #define HGLFT_ERRORHELP_VAR "hglft_errorHelp"      /* Print explanatory text */
 #define HGLFT_REFRESHONLY_VAR "hglft_doRefreshOnly"      /* Just refresh drop-down lists */
 #define HGLFT_LAST_CHAIN "hglft_lastChain"
 
 /* liftOver options: */
 #define HGLFT_MINMATCH "hglft_minMatch"          
@@ -436,31 +435,30 @@
 if (cgiOptionalString(HGLFT_ERRORHELP_VAR))
     {
     puts("<PRE>");
     puts(liftOverErrHelp());
     puts("</PRE>");
     return;
     }
 
 /* Get data to convert - from userData variable, or if 
  * that is empty from a file. */
 
 if (cartOptionalString(cart, "SubmitFile"))
     userData = cartOptionalString(cart, HGLFT_DATAFILE_VAR);
 else
     userData = cartOptionalString(cart, HGLFT_USERDATA_VAR);
-userData = windowsToAscii(userData);
 cartWebStart(cart, NULL, "Lift Genome Annotations");
 
 getDbAndGenome(cart, &db, &organism, oldVars);
 
 chainList = liftOverChainList();
 
 choice = defaultChoices(chainList, db);
 thisChain = chainStringVal(choice);
 if (choice == NULL)
     errAbort("Sorry, no conversions available from this assembly\n");
 
 minSizeQ = cartCgiUsualInt(cart, HGLFT_MINSIZEQ, choice->minSizeQ);
 minChainT = cartCgiUsualInt(cart, HGLFT_MINCHAINT, choice->minChainT);
 minBlocks = cartCgiUsualDouble(cart, HGLFT_MINBLOCKS, choice->minBlocks);
 minMatch = cartCgiUsualDouble(cart, HGLFT_MINMATCH, choice->minMatch);