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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
default: runtests
TOP ?= $(abspath ../..)
MODULE = test/ngs-pileup
TEST_TOOLS = \
test-ngs-pileup
include $(TOP)/build/Makefile.env
$(TEST_TOOLS): makedirs
@ $(MAKE_CMD) $(TEST_BINDIR)/$@
.PHONY: $(TEST_TOOLS)
clean: stdclean
#-------------------------------------------------------------------------------
# test-ngs-pileup
#
TEST_NGS_PILEUP_SRC = \
test-ngs-pileup
TEST_NGS_PILEUP_OBJ = \
$(addsuffix .$(OBJX),$(TEST_NGS_PILEUP_SRC))
TEST_NGS_PILEUP_LIB = \
-sngs-c++ \
-sncbi-ngs-c++ \
-sncbi-vdb \
-skapp \
-sktst \
$(TEST_BINDIR)/test-ngs-pileup: $(TEST_NGS_PILEUP_OBJ)
$(LP) --exe -o $@ $^ $(TEST_NGS_PILEUP_LIB)
#-------------------------------------------------------------------------------
# slowtests: match output vs sra-pileup
#
slowtests: diff-vs-sra-pileup
diff-vs-sra-pileup:
-@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 1.0 SRR833251
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 2.0 SRR1166393
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 3.0 ERR334733 # ILLUMINA
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 4.0 SRR1068006
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 5.0 SRR619510 # ABSOLID REF_ROWS=36172
-@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 6.0 SRR1251988 # SEC_ROWS=198
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 7.0 SRR1186012 # ION_TORRENT
-@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 8.1 SRR556739 -r chrY # COMPLETE_GENOMICS
-@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 8.2 SRR556739 -r chrM # COMPLETE_GENOMICS, circular reference
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 9.0 SRR341578 -r NC_011752.1 #:19900-20022
onediff:
@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 9.1 SRR341578 -r NC_011752.1:19900-20022
#alignment selection:
#TODO: multiple references in one accession
#TODO: multiple accessions with overlapping alignments
#TODO: filter by reference (-r ref) using canonic name
#TODO: filter by reference (-r ref) using common name
#TODO: filter by multiple references (-r ref1 -r ref2)
#TODO: filter by position on the reference (-r ref:from-to)
#TODO: filter by multiple positions on the same reference (-r ref:from1-to1 -r ref:from2-to2)
#TODO: primary alignment table only (-t p)
#TODO: secondary alignment table only (-t s)
#TODO: evidence table only (-t e)
#TODO: include duplicates (-d 1)
#TODO: do not include duplicates (-d 0) NB: broken in sra-pileup
#TODO: minimum mapq value (-q min)
#output control:
#TODO: omit qualities (-n)
#output file control:
#TODO: redirect output to a file (-o)
#TODO: bzip2 output (--bzip2)
#TODO: gzip output (--gzip)
# hidden options:
#TODO: output alignment information (-i)
# any more?
#not sure if these are needed:
# -p|--spotgroups <spotgroups-modes> divide by spotgroups
# -e|--seqname use original seq-name
# --minmismatch min percent of mismatches used in function
# mismatch, default is 5%
# --merge-dist If adjacent slices are closer than this,
# they are merged and skiplist is created.
# a value of zero disables the feature,
# default is 10000
# --function ref list references
# --function ref-ex list references coverage
# --function count sort pileup with counters
# --function stat strand/tlen statistic
# --function mismatch only lines with mismatch
# --function index list deletion counts
# --function varcount variation counters: ref-name, ref-pos,
# ref-base, coverage, mismatch A, mismatch C,
# mismatch G, mismatch T, deletes, inserts, ins
# after A, ins after C, ins after G, ins
# after T
# --function deletes list deletions greater then 20
#
#Grouping of accessions into artificial spotgroups:
# sra-pileup SRRXXXXXX=a SRRYYYYYY=b SRRZZZZZZ=a
.PHONY: diff-vs-sra-pileup
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