[med-svn] [Git][med-team/vt][master] Commit NMU by Adrian Bunk

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / vt


Commits:
73a50b1d by Andreas Tille at 2020-11-05T20:50:00+01:00
Commit NMU by Adrian Bunk

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/0001-updated-faidx_fetch_uc_seq.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+vt (0.57721+ds-2.1) unstable; urgency=low
+
+  * Non-maintainer upload.
+  * Change the build dependency to libcurl4-gnutls-dev.
+    (Closes: #971793)
+  * Backport upstream fix for FTBFS with latest HTSlib.
+
+ -- Adrian Bunk <bunk at debian.org>  Thu, 05 Nov 2020 10:49:14 +0200
+
 vt (0.57721+ds-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),
                zlib1g-dev,
                libbz2-dev,
                liblzma-dev,
-               libcurl4-openssl-dev,
+               libcurl4-gnutls-dev,
                libssl-dev,
                libdeflate-dev,
                libhts-dev,


=====================================
debian/patches/0001-updated-faidx_fetch_uc_seq.patch
=====================================
@@ -0,0 +1,94 @@
+From 6a0e555b88fd385e4ace6f477779a97e3fd4e594 Mon Sep 17 00:00:00 2001
+From: Adrian Tan <atks at umich.edu>
+Date: Fri, 13 Jul 2018 17:20:56 -0400
+Subject: updated faidx_fetch_uc_seq
+
+diff --git a/hts_utils.cpp b/hts_utils.cpp
+index 6644f0e..30bf37a 100644
+--- a/hts_utils.cpp
++++ b/hts_utils.cpp
+@@ -40,37 +40,53 @@ typedef khash_t(vdict) vdict_t;
+  */
+ char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
+ {
+-    int l;
+-    char c;
+-    khiter_t iter;
+-    faidx1_t val;
+-    char *seq=NULL;
+-
+-    // Adjust position
+-    iter = kh_get(s, fai->hash, c_name);
+-    if(iter == kh_end(fai->hash)) return 0;
+-    val = kh_value(fai->hash, iter);
+-    if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+-    if(p_beg_i < 0) p_beg_i = 0;
+-    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+-    if(p_end_i < 0) p_end_i = 0;
+-    else if(val.len <= p_end_i) p_end_i = val.len - 1;
+-
+-    // Now retrieve the sequence
+-    int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+-    if ( ret<0 )
+-    {
+-        *len = -1;
+-        fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
+-        return NULL;
+-    }
+-    l = 0;
+-    seq = (char*)malloc(p_end_i - p_beg_i + 2);
+-    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
+-        if (isgraph(c)) seq[l++] = toupper(c);
+-    seq[l] = '\0';
+-    *len = l;
++    char* seq = faidx_fetch_seq(fai, c_name, p_beg_i, p_end_i, len);
++   
++   
++   //    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
++//        if (isgraph(c)) seq[l++] = toupper(c);
++//    seq[l] = '\0';
++//    *len = l;
++    
++    for (int32_t i=0; i<*len; ++i)
++    {
++        if (isgraph(seq[i])) seq[i] = toupper(seq[i]);
++    }
++    
+     return seq;
++    
++    
++//    int l;
++//    char c;
++//    khiter_t iter;
++//    faidx1_t val;
++//    char *seq=NULL;
++//
++//    // Adjust position
++//    iter = kh_get(s, fai->hash, c_name);
++//    if(iter == kh_end(fai->hash)) return 0;
++//    val = kh_value(fai->hash, iter);
++//    if(p_end_i < p_beg_i) p_beg_i = p_end_i;
++//    if(p_beg_i < 0) p_beg_i = 0;
++//    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
++//    if(p_end_i < 0) p_end_i = 0;
++//    else if(val.len <= p_end_i) p_end_i = val.len - 1;
++//
++//    // Now retrieve the sequence
++//    int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
++//    if ( ret<0 )
++//    {
++//        *len = -1;
++//        fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
++//        return NULL;
++//    }
++//    l = 0;
++//    seq = (char*)malloc(p_end_i - p_beg_i + 2);
++//    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
++//        if (isgraph(c)) seq[l++] = toupper(c);
++//    seq[l] = '\0';
++//    *len = l;
++//    return seq;
+ }
+ 
+ /**********
+


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 makefile
 fix-spelling
 test-fail-on-error
+0001-updated-faidx_fetch_uc_seq.patch



View it on GitLab: https://salsa.debian.org/med-team/vt/-/commit/73a50b1d13545bdf058829a7159ae720c8131407

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