From 40553a2a863a1c1c01b4cae762ea6ab2351e10f4 Mon Sep 17 00:00:00 2001 From: =?utf8?q?=C3=89tienne=20Mollier?= Date: Sat, 19 Nov 2022 11:34:57 +0100 Subject: [PATCH] test-truncated-bam.patch: delete; applied upstream. --- debian/patches/series | 1 - debian/patches/test-truncated-bam.patch | 28 ------------------------- 2 files changed, 29 deletions(-) delete mode 100644 debian/patches/test-truncated-bam.patch diff --git a/debian/patches/series b/debian/patches/series index 87dc4c2..43ee385 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ skip_test_remote.patch clean_less skip-test-on-32-bit.patch -test-truncated-bam.patch diff --git a/debian/patches/test-truncated-bam.patch b/debian/patches/test-truncated-bam.patch deleted file mode 100644 index ae282ba..0000000 --- a/debian/patches/test-truncated-bam.patch +++ /dev/null @@ -1,28 +0,0 @@ -Description: Truncate ex2.bam irrespective of its size - The Makefile also builds ex2.bam from ex2.sam via `samtools view`. - Samtools as traditionally built using zlib typically generates a - 124703-byte file, whereas when built using libdeflate it typically - generates a 122804-byte file -- but `head -c 124000` leaves that unchanged - and the test cases fail because ex2_truncated.bam is unexpectedly valid. - . - Rewrite the truncation rule to remove the final 512 bytes, irrespective - of ex2.bam's length. (No practical compression will reduce it to less - than 512 bytes in total, so this is safe.) Fixes #1128. -Author: John Marshall -Bug: https://github.com/pysam-developers/pysam/issues/1128 -Applied-Upstream: 56b1624c21b02762fdcea3aa5f657a4152ca178e -Reviewed-by: Étienne Mollier -Last-Update: 2022-10-02 ---- -This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- python-pysam.orig/tests/pysam_data/Makefile -+++ python-pysam/tests/pysam_data/Makefile -@@ -70,7 +70,7 @@ - samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz - - ex2_truncated.bam: ex2.bam -- head -c 124000 ex2.bam > ex2_truncated.bam -+ dd if=ex2.bam of=ex2_truncated.bam bs=$$((`wc -c < ex2.bam`-512)) count=1 - - # Append a corrupt read with block_size < sizeof(bam_core_t fields) - ex2_corrupt.bam: ex2.bam -- 2.30.2