From b95bed7e966ddf8b0b03eeff121f9f94bb4653f7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Sat, 4 Jan 2020 18:31:13 +0100 Subject: [PATCH] =?utf8?q?samtools=20import=20=E2=86=92=20=20samtools=20vi?= =?utf8?q?ew?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- debian/changelog | 7 +++++++ debian/patches/hts1.10 | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+) diff --git a/debian/changelog b/debian/changelog index 9f451b4..0f1afed 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +python-pysam (0.15.3+ds-2) UNRELEASED; urgency=medium + + * Team upload. + * Update deprecated samtools import test commands to samtools view + + -- Michael R. Crusoe Sat, 04 Jan 2020 18:31:16 +0100 + python-pysam (0.15.3+ds-1) unstable; urgency=medium * Team upload. diff --git a/debian/patches/hts1.10 b/debian/patches/hts1.10 index 1f563ef..4909529 100644 --- a/debian/patches/hts1.10 +++ b/debian/patches/hts1.10 @@ -45,3 +45,43 @@ Description: Remove symbol that was removed in libhts3 elif self.htsfile.format.format == cram: with nogil: ret = htell(cram_fd_get_fp(self.htsfile.fp.cram)) +--- python-pysam.orig/tests/00README.txt ++++ python-pysam/tests/00README.txt +@@ -15,7 +15,7 @@ + To try samtools, you may run the following commands: + + samtools faidx ex1.fa # index the reference FASTA +- samtools import ex1.fa.fai ex1.sam.gz ex1.bam # SAM->BAM ++ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz # SAM->BAM + samtools index ex1.bam # index BAM + samtools tview ex1.bam ex1.fa # view alignment + samtools pileup -cf ex1.fa ex1.bam # pileup and consensus +--- python-pysam.orig/tests/pysam_data/Makefile ++++ python-pysam/tests/pysam_data/Makefile +@@ -32,7 +32,7 @@ + samtools calmd --output-fmt BAM $^ > $@ + + #%.bam: %.sam ex1.fa.fai +-# samtools import ex1.fa.fai $< $@ ++# samtools view -bt ex1.fa.fai -i $@ $< + + uncompressed.bam: ex2.sam + samtools view -buS $< > $@ +@@ -53,7 +53,7 @@ + samtools faidx ex1.fa + + ex1.bam:ex1.sam.gz ex1.fa.fai +- samtools import ex1.fa.fai ex1.sam.gz ex1.bam ++ samtools view -bt ex1.fa.fai -o ex1.bam ex1.sam.gz + + %.bam.bai:%.bam + samtools index $< +@@ -73,7 +73,7 @@ + + example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam + touch tmp.list +- samtools import tmp.list $< $@ ++ samtools view -bt tmp.list -o $@ $< + rm -f tmp.list + + example_bai.bam: ex1.bam -- 2.30.2