[med-svn] [Git][med-team/samtools][master] adapted patches, mahem patch was applied upstream

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / samtools


Commits:
619dfea0 by Andreas Tille at 2018-02-14T13:21:56+01:00
adapted patches, mahem patch was applied upstream

- - - - -


4 changed files:

- debian/changelog
- − debian/patches/mayhem.patch
- debian/patches/series
- debian/patches/sort-tests-memory-limit.patch


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,7 +1,6 @@
 samtools (1.7-1) UNRELEASED; urgency=medium
 
-  * New upstream version
-  TODO: Adpapt patches
+  * New upstream version (adapted patches, mahem patch was applied upstream)
   * Standards-Version: 4.1.3
 
  -- Andreas Tille <tille at debian.org>  Wed, 14 Feb 2018 09:50:58 +0100


=====================================
debian/patches/mayhem.patch deleted
=====================================
--- a/debian/patches/mayhem.patch
+++ /dev/null
@@ -1,71 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 21 Dec 2015 13:20:46 +0100
-Bug-Debian: https://bugs.debian.org/716197
-            https://bugs.debian.org/716199
-Description: Fix Mayhem issues caused by unlimited reads of gz input
-Forwarded: https://github.com/samtools/samtools/issues/751
-Comment: Applied upstream
-          https://github.com/samtools/samtools/commit/10cc08958bcbbd47d2c3deb81881fcb12ec3a71e
-
---- a/misc/maq2sam.c
-+++ b/misc/maq2sam.c
-@@ -99,14 +99,37 @@ maqmap_t *maqmap_read_header(gzFile fp)
-         }
-         assert(mm->format == MAQMAP_FORMAT_NEW);
-     }
--    gzread(fp, &mm->n_ref, sizeof(int));
-+    if ( gzread(fp, &mm->n_ref, sizeof(int)) < sizeof(int)) {
-+        fprintf(stderr, "To few bytes in input file");
-+        return NULL;
-+    }
-+    if (mm->n_ref < 0) {
-+        fprintf(stderr, "Incorrect n_ref read from input file\n");
-+        return NULL;
-+    }
-+    if ( gzeof(fp) ) {
-+        fprintf(stderr, "Unexpected end of file.");
-+        return NULL;
-+    }
-     mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
-     for (k = 0; k != mm->n_ref; ++k) {
-+        if ( gzeof(fp) ) {
-+            fprintf(stderr, "Unexpected end of file.");
-+            return NULL;
-+        }
-         gzread(fp, &len, sizeof(int));
-         mm->ref_name[k] = (char*)malloc(len * sizeof(char));
-+        if ( gzeof(fp) ) {
-+            fprintf(stderr, "Unexpected end of file.");
-+            return NULL;
-+        }
-         gzread(fp, mm->ref_name[k], len);
-     }
-     /* read number of mapped reads */
-+    if ( gzeof(fp) ) {
-+        fprintf(stderr, "Unexpected end of file.");
-+        return NULL;
-+    }
-     gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
-     return mm;
- }
-@@ -118,6 +141,8 @@ void maq2tam_core(gzFile fp, const char
-     int ret;
-     m1 = &mm1;
-     mm = maqmap_read_header(fp);
-+    if (!mm) exit(1);
-+
-     while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
-         int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
-         if (m1->flag) flag |= 1;
-@@ -192,6 +217,11 @@ int main(int argc, char *argv[])
-         return 1;
-     }
-     fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
-+    if (!fp ) {
-+        fprintf(stderr, "Unable to open file %s", argv[1]);
-+        fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
-+        return 1;
-+    }
-     maq2tam_core(fp, argc > 2? argv[2] : 0);
-     gzclose(fp);
-     return 0;


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 spelling.patch
-mayhem.patch
 sort-tests-memory-limit.patch


=====================================
debian/patches/sort-tests-memory-limit.patch
=====================================
--- a/debian/patches/sort-tests-memory-limit.patch
+++ b/debian/patches/sort-tests-memory-limit.patch
@@ -6,7 +6,7 @@ Last-Update: 2017-12-22
 
 --- a/test/test.pl
 +++ b/test/test.pl
-@@ -2465,22 +2465,22 @@
+@@ -2472,22 +2472,22 @@ sub test_sort
  
  
      # Pos sort



View it on GitLab: https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd

---
View it on GitLab: https://salsa.debian.org/med-team/samtools/commit/619dfea0f5b4ff44b577749fb03287c642d4ddbd
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180214/bbdf643c/attachment-0001.html>