[med-svn] [Git][med-team/vt][master] 2 commits: patch 0001: Get rid of commented code

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / vt


Commits:
4df59f7e by Antoni Villalonga at 2020-11-09T07:47:35+01:00
patch 0001: Get rid of commented code

- - - - -
c9a3a2be by Andreas Tille at 2020-11-09T08:02:03+00:00
Merge branch 'patch-0001-amend' into 'master'

patch 0001: Get rid of commented code

See merge request med-team/vt!1
- - - - -


1 changed file:

- debian/patches/0001-updated-faidx_fetch_uc_seq.patch


Changes:

=====================================
debian/patches/0001-updated-faidx_fetch_uc_seq.patch
=====================================
@@ -3,11 +3,9 @@ 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;
+@@ -40,36 +40,14 @@
   */
  char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
  {
@@ -30,65 +28,23 @@ index 6644f0e..30bf37a 100644
 -    // 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 )
--    {
++    char* seq = faidx_fetch_seq(fai, c_name, p_beg_i, p_end_i, len);
++   
++    
++    for (int32_t i=0; i<*len; ++i)
+     {
 -        *len = -1;
 -        fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
 -        return NULL;
--    }
++        if (isgraph(seq[i])) seq[i] = toupper(seq[i]);
+     }
 -    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;
  }
  
- /**********
-



View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/73a50b1d13545bdf058829a7159ae720c8131407...c9a3a2be69f779509142f49346a01d16dea93f75

-- 
View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/73a50b1d13545bdf058829a7159ae720c8131407...c9a3a2be69f779509142f49346a01d16dea93f75
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