Use official htslib in libucsc

# use_debian_packaged_htslib.patch

unbundle-htslib.patch

Author: John Marshall <John.W.Marshall@glasgow.ac.uk>

Last-Update: Fri Jan 24 14:34:54 GMT 2020

Description: Use official htslib in libucsc

Origin: https://alioth-lists.debian.net/pipermail/debian-med-packaging/2020-January/077104.html

--- a/src/lib/bamFile.c

+++ b/src/lib/bamFile.c

@@ -7,10 +7,7 @@

 #include "portable.h"

 #include "bamFile.h"

 #include "htmshell.h"

-#include "cram/cram_samtools.h"

-#include "cram/sam_header.h"

-#include "cram/cram_structs.h"

-#include "htslib/cram.h"

+#include "htslib/sam.h"

 #include "udc.h"

 #include "psl.h"

@@ -179,44 +176,6 @@ if (iter == NULL)

 int result;

 while ((result = sam_itr_next(samfile, iter, b)) >= 0) 

     callbackFunc(b, callbackData, header);

-

-// if we're reading a CRAM file and the MD5 string has been set

-// we know there was an error finding the reference and we need

-// to request that it be loaded.

-if (samfile->format.format == cram) 

-    {

-    char *md5String =  cram_get_Md5(samfile);

-    if (!isEmpty(md5String))

-        {

-        char server[4096];

-        char pendingFile[4096];

-        char errorFile[4096];

-

-        char *refPath = cram_get_ref_url(samfile);

-        char *cacheDir = cram_get_cache_dir(samfile);

-

-        sprintf(server, refPath, md5String);

-        sprintf(pendingFile, "%s/pending/",cacheDir);

-        sprintf(errorFile, "%s/error/%s",cacheDir,md5String);

-        makeDirsOnPath(pendingFile);

-        sprintf(pendingFile, "%s/pending/%s",cacheDir,md5String);

-        FILE *downFile;

-        if ((downFile = fopen(errorFile, "r")) != NULL)

-            {

-            char errorBuf[4096];

-            mustGetLine(downFile, errorBuf, sizeof errorBuf);

-            errAbort("cannot find reference %s.  Error: %s\n", md5String,errorBuf);

-            }

-        else

-            {

-            if ((downFile = fopen(pendingFile, "w")) == NULL)

-                errAbort("cannot find reference %s.  Cannot create file %s.",md5String, pendingFile);  

-            fprintf(downFile,  "%s\n", server);

-            fclose(downFile);

-            errAbort("Cannot find reference %s.  Downloading from %s. Please refresh screen to check download status.",md5String, server);

-            }

-        }

-    }

 }

 void bamAndIndexFetchPlus(char *fileOrUrl, char *baiFileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,

@@ -231,12 +190,6 @@ void bamAndIndexFetchPlus(char *fileOrUr

 {

 char *bamFileName = NULL;

 samfile_t *fh = bamOpen(fileOrUrl, &bamFileName);

-if (fh->format.format == cram) 

-    {

-    if (cacheDir == NULL)

-        errAbort("CRAM cache dir hg.conf variable (cramRef) must exist for CRAM support");

-    cram_set_cache_url(fh, cacheDir, refUrl);  

-    }

 bam_hdr_t *header = sam_hdr_read(fh);

 if (pSamFile != NULL)

     *pSamFile = fh;

@@ -256,16 +209,9 @@ static int bamGetTargetCount(char *fileO

 {

 int tCount = 0;

 htsFile *htsF = hts_open(fileOrUrl, "r");

-if (htsF->format.format == crai)

-    {

-    SAM_hdr *cramHdr = cram_fd_get_header(htsF->fp.cram);

-    tCount = cramHdr->nref;

-    }

-else

-    {

-    bam_hdr_t *bamHdr = bam_hdr_read(htsF->fp.bgzf);

-    tCount = bamHdr->n_targets;

-    }

+bam_hdr_t *bamHdr = sam_hdr_read(htsF);

+tCount = bamHdr->n_targets;

+bam_hdr_destroy(bamHdr);

 hts_close(htsF);

 return tCount;

 }