Andreas Tille pushed to branch master at Debian Med / libucsc
Commits: f6cc218e by Andreas Tille at 2020-01-27T08:35:53+01:00 Use official htslib in libucsc - - - - - 2 changed files: - debian/patches/series - + debian/patches/unbundle-htslib.patch Changes: ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ # use_debian_packaged_htslib.patch +unbundle-htslib.patch ===================================== debian/patches/unbundle-htslib.patch ===================================== @@ -0,0 +1,97 @@ +Author: John Marshall <[email protected]> +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; + } View it on GitLab: https://salsa.debian.org/med-team/libucsc/commit/f6cc218e9af7e655959bea16a2c80067f806267e -- View it on GitLab: https://salsa.debian.org/med-team/libucsc/commit/f6cc218e9af7e655959bea16a2c80067f806267e You're receiving this email because of your account on salsa.debian.org.
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