Control: tags 971793 + patch
Control: tags 971793 + pending
Dear maintainer,
I've prepared an NMU for vt (versioned as 0.57721+ds-2.1) and uploaded
it to DELAYED/14. Please feel free to tell me if I should cancel it.
cu
Adrian
diff -Nru vt-0.57721+ds/debian/changelog vt-0.57721+ds/debian/changelog
--- vt-0.57721+ds/debian/changelog 2020-07-13 15:57:56.000000000 +0300
+++ vt-0.57721+ds/debian/changelog 2020-11-05 10:49:14.000000000 +0200
@@ -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 <b...@debian.org> Thu, 05 Nov 2020 10:49:14 +0200
+
vt (0.57721+ds-2) unstable; urgency=medium
* Team upload.
diff -Nru vt-0.57721+ds/debian/control vt-0.57721+ds/debian/control
--- vt-0.57721+ds/debian/control 2020-07-13 15:57:56.000000000 +0300
+++ vt-0.57721+ds/debian/control 2020-11-05 10:49:14.000000000 +0200
@@ -7,7 +7,7 @@
zlib1g-dev,
libbz2-dev,
liblzma-dev,
- libcurl4-openssl-dev,
+ libcurl4-gnutls-dev,
libssl-dev,
libdeflate-dev,
libhts-dev,
diff -Nru vt-0.57721+ds/debian/patches/0001-updated-faidx_fetch_uc_seq.patch vt-0.57721+ds/debian/patches/0001-updated-faidx_fetch_uc_seq.patch
--- vt-0.57721+ds/debian/patches/0001-updated-faidx_fetch_uc_seq.patch 1970-01-01 02:00:00.000000000 +0200
+++ vt-0.57721+ds/debian/patches/0001-updated-faidx_fetch_uc_seq.patch 2020-11-05 10:49:14.000000000 +0200
@@ -0,0 +1,94 @@
+From 6a0e555b88fd385e4ace6f477779a97e3fd4e594 Mon Sep 17 00:00:00 2001
+From: Adrian Tan <a...@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;
+ }
+
+ /**********
+
diff -Nru vt-0.57721+ds/debian/patches/series vt-0.57721+ds/debian/patches/series
--- vt-0.57721+ds/debian/patches/series 2020-07-13 15:57:56.000000000 +0300
+++ vt-0.57721+ds/debian/patches/series 2020-11-05 10:49:14.000000000 +0200
@@ -1,3 +1,4 @@
makefile
fix-spelling
test-fail-on-error
+0001-updated-faidx_fetch_uc_seq.patch
