Changeset 3472


Ignore:
Timestamp:
Mar 4, 2016, 6:49:33 AM (6 years ago)
Author:
Peter
Message:

generate sorted bam file directly from unsorted sam file; skip intermediate unsorted bam file.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/test/Makefile.am

    r3471 r3472  
    316316
    317317if HAVE_SAMTOOLS_EXECUTABLE
    318 test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
     318test/data/foo.sorted.bam: test/data/foo.sam
    319319  $(AM_V_GEN)
    320   $(AM_V_at)$(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam \
    321   > $@-t && mv $@-t $@
    322 
    323 test/data/foo.sorted.bam: test/data/foo.bam
    324   $(AM_V_GEN)
    325   $(AM_V_at)$(SAMTOOLS) sort -o $@ test/data/foo.bam
     320  $(AM_V_at)$(SAMTOOLS) sort -o $@ $(srcdir)/test/data/foo.sam
    326321
    327322test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
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