1# =========================================================================== 2# 3# PUBLIC DOMAIN NOTICE 4# National Center for Biotechnology Information 5# 6# This software/database is a "United States Government Work" under the 7# terms of the United States Copyright Act. It was written as part of 8# the author's official duties as a United States Government employee and 9# thus cannot be copyrighted. This software/database is freely available 10# to the public for use. The National Library of Medicine and the U.S. 11# Government have not placed any restriction on its use or reproduction. 12# 13# Although all reasonable efforts have been taken to ensure the accuracy 14# and reliability of the software and data, the NLM and the U.S. 15# Government do not and cannot warrant the performance or results that 16# may be obtained by using this software or data. The NLM and the U.S. 17# Government disclaim all warranties, express or implied, including 18# warranties of performance, merchantability or fitness for any particular 19# purpose. 20# 21# Please cite the author in any work or product based on this material. 22# 23# =========================================================================== 24 25default: runtests 26 27TOP ?= $(abspath ../..) 28 29MODULE = test/ngs-pileup 30 31TEST_TOOLS = \ 32 test-ngs-pileup 33 34include $(TOP)/build/Makefile.env 35 36$(TEST_TOOLS): makedirs 37 @ $(MAKE_CMD) $(TEST_BINDIR)/$@ 38 39.PHONY: $(TEST_TOOLS) 40 41clean: stdclean 42 43#------------------------------------------------------------------------------- 44# test-ngs-pileup 45# 46TEST_NGS_PILEUP_SRC = \ 47 test-ngs-pileup 48 49TEST_NGS_PILEUP_OBJ = \ 50 $(addsuffix .$(OBJX),$(TEST_NGS_PILEUP_SRC)) 51 52TEST_NGS_PILEUP_LIB = \ 53 -sngs-c++ \ 54 -sncbi-ngs-c++ \ 55 -sncbi-vdb-static \ 56 -skapp \ 57 -sktst \ 58 59$(TEST_BINDIR)/test-ngs-pileup: $(TEST_NGS_PILEUP_OBJ) 60 $(LP) --exe -o $@ $^ $(TEST_NGS_PILEUP_LIB) 61 62#------------------------------------------------------------------------------- 63# slowtests: match output vs sra-pileup 64# 65 66slowtests: diff-vs-sra-pileup 67 68diff-vs-sra-pileup: 69 -@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 1.0 SRR833251 70 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 2.0 SRR1166393 71 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 3.0 ERR334733 # ILLUMINA 72 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 4.0 SRR1068006 73 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 5.0 SRR619510 # ABSOLID REF_ROWS=36172 74 -@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 6.0 SRR1251988 # SEC_ROWS=198 75 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 7.0 SRR1186012 # ION_TORRENT 76 -@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 8.1 SRR556739 -r chrY # COMPLETE_GENOMICS 77 -@ ./runtestcase.sh $(BINDIR) $(SRCDIR) 8.2 SRR556739 -r chrM # COMPLETE_GENOMICS, circular reference 78 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 9.0 SRR341578 -r NC_011752.1 #:19900-20022 79 80onediff: 81 @ ./runtestcase.sh $(BINDIR) $(SRCDIR) 9.1 SRR341578 -r NC_011752.1:19900-20022 82 83#alignment selection: 84#TODO: multiple references in one accession 85#TODO: multiple accessions with overlapping alignments 86#TODO: filter by reference (-r ref) using canonic name 87#TODO: filter by reference (-r ref) using common name 88#TODO: filter by multiple references (-r ref1 -r ref2) 89#TODO: filter by position on the reference (-r ref:from-to) 90#TODO: filter by multiple positions on the same reference (-r ref:from1-to1 -r ref:from2-to2) 91#TODO: primary alignment table only (-t p) 92#TODO: secondary alignment table only (-t s) 93#TODO: evidence table only (-t e) 94#TODO: include duplicates (-d 1) 95#TODO: do not include duplicates (-d 0) NB: broken in sra-pileup 96#TODO: minimum mapq value (-q min) 97 98#output control: 99#TODO: omit qualities (-n) 100 101#output file control: 102#TODO: redirect output to a file (-o) 103#TODO: bzip2 output (--bzip2) 104#TODO: gzip output (--gzip) 105 106# hidden options: 107#TODO: output alignment information (-i) 108# any more? 109 110#not sure if these are needed: 111# -p|--spotgroups <spotgroups-modes> divide by spotgroups 112# -e|--seqname use original seq-name 113# --minmismatch min percent of mismatches used in function 114# mismatch, default is 5% 115# --merge-dist If adjacent slices are closer than this, 116# they are merged and skiplist is created. 117# a value of zero disables the feature, 118# default is 10000 119# --function ref list references 120# --function ref-ex list references coverage 121# --function count sort pileup with counters 122# --function stat strand/tlen statistic 123# --function mismatch only lines with mismatch 124# --function index list deletion counts 125# --function varcount variation counters: ref-name, ref-pos, 126# ref-base, coverage, mismatch A, mismatch C, 127# mismatch G, mismatch T, deletes, inserts, ins 128# after A, ins after C, ins after G, ins 129# after T 130# --function deletes list deletions greater then 20 131# 132#Grouping of accessions into artificial spotgroups: 133# sra-pileup SRRXXXXXX=a SRRYYYYYY=b SRRZZZZZZ=a 134 135 136 137.PHONY: diff-vs-sra-pileup 138