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 <ti...@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 <ti...@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.
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