samtools import → samtools view

diff --git a/debian/changelog b/debian/changelog
index 9f451b40a0e45932b7ae48d7e7bd067149b83872..0f1afed4a554f5ffda7380683a445d0f5c5fa610 100644 (file)
--- 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 <michael.crusoe@gmail.com>  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 1f563efaccc97e0bd490d23ce6a5894a8b084bed..490952933f82fe41cac00766c1e141c0f693941c 100644 (file)
--- 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