1# HMMER's test suite, in sqc command format 2# 3# See the ../easel/devkit/sqc script for documentation of sqc. 4# 5# Usage: 6# sqc <level> testsuite.sqc <top_builddir> <top_srcdir> 7# Example: 8# cd build-debug 9# sqc 1 ../testsuite/valgrind.sqc . .. 10# 11# level 1 = the standard test suite 12# level 2 = (currently nothing) 13# level 3 = valgrind tests 14# 15# Remember, sqc does three types of file substitution on this file: 16# @foo@ = executables in the build directory => top_builddir/foo 17# !foo! = data files in the source directory => top_srcdir/foo 18# %FOO% = tmp files, created, managed, cleaned up by sqc itself 19# 20 21 22################################################################ 23# Unit test drivers for each .c file 24################################################################ 25 261 exercise hmmer @src/hmmer_utest@ 271 exercise build @src/build_utest@ 281 exercise generic_fwdback @src/generic_fwdback_utest@ 291 exercise generic_msv @src/generic_msv_utest@ 301 exercise generic_stotrace @src/generic_stotrace_utest@ 311 exercise generic_viterbi @src/generic_viterbi_utest@ 321 exercise hmmd_search_status @src/hmmd_search_status_utest@ 331 exercise logsum @src/logsum_utest@ 341 exercise modelconfig @src/modelconfig_utest@ 351 exercise seqmodel @src/seqmodel_utest@ 361 exercise p7_alidisplay @src/p7_alidisplay_utest@ 371 exercise p7_bg @src/p7_bg_utest@ 381 exercise p7_domain @src/p7_domain_utest@ 391 exercise p7_gmx @src/p7_gmx_utest@ 401 exercise p7_hit @src/p7_hit_utest@ 411 exercise p7_hmm @src/p7_hmm_utest@ 421 exercise p7_hmmfile @src/p7_hmmfile_utest@ 431 exercise p7_hmmd_search_stats @src/p7_hmmd_search_stats_utest@ 441 exercise p7_profile @src/p7_profile_utest@ 451 exercise p7_tophits @src/p7_tophits_utest@ 461 exercise p7_trace @src/p7_trace_utest@ 471 exercise p7_scoredata @src/p7_scoredata_utest@ 48 49 501 exercise decoding @src/impl/decoding_utest@ 511 exercise fwdback @src/impl/fwdback_utest@ 521 exercise io @src/impl/io_utest@ 531 exercise msvfilter @src/impl/msvfilter_utest@ 541 exercise null2 @src/impl/null2_utest@ 551 exercise optacc @src/impl/optacc_utest@ 561 exercise stotrace @src/impl/stotrace_utest@ 571 exercise vitfilter @src/impl/vitfilter_utest@ 581 exercise hmmpgmd2msa @src/hmmpgmd2msa_utest@ !testsuite/Caudal_act.hmm! 59# Still to come, unit tests for 60# emit.c 61# errors.c 62# evalues.c 63# eweight.c 64# heatmap.c 65# hmmer.c 66# island.c 67# modelstats.c 68# mpisupport.c (MPI testing needs to be handled specially) 69# p7_bg.c 70# p7_domaindef.c 71# p7_prior.c 72# p7_spensemble.c 73 74 75################################################################ 76# Option tests 77################################################################ 78 79# Prep a press'ed "minifam" that's used here and also in some integration tests, 80# and extract an individual 'typical' model Caudal_act. 811 prep Caudal @easel/miniapps/esl-afetch@ !testsuite/minifam! Caudal_act > %CAUDAL.STO% 821 prep hmm @src/hmmbuild@ %CAUDAL.HMM% %CAUDAL.STO% 831 prep minifam @src/hmmbuild@ %MINIFAM.HMM% !testsuite/minifam! 841 prep minifam_press @src/hmmpress@ %MINIFAM.HMM% 85 86 87# hmmalign xxxxxxxxxxxxxxxxxxxx 881 prep testseq @src/hmmemit@ -p --unilocal -L0 -N 4 --seed 42 !testsuite/Caudal_act.hmm! > %TESTSEQ% 891 exercise hmmalign @src/hmmalign@ !testsuite/Caudal_act.hmm! %TESTSEQ% 901 exercise hmmalign/-h @src/hmmalign@ -h 911 exercise hmmalign/-o @src/hmmalign@ -o /dev/null !testsuite/Caudal_act.hmm! %TESTSEQ% 921 exercise hmmalign/--mapali @src/hmmalign@ --mapali !testsuite/Caudal_act.sto! !testsuite/Caudal_act.hmm! %TESTSEQ% 931 exercise hmmalign/--trim @src/hmmalign@ --trim !testsuite/Caudal_act.hmm! %TESTSEQ% 941 exercise hmmalign/--amino @src/hmmalign@ --amino !testsuite/Caudal_act.hmm! %TESTSEQ% 951 exercise hmmalign/--informat @src/hmmalign@ --informat fasta !testsuite/Caudal_act.hmm! %TESTSEQ% 961 exercise hmmalign/--outformat @src/hmmalign@ --outformat a2m !testsuite/Caudal_act.hmm! %TESTSEQ% 97 98# hmmbuild xxxxxxxxxxxxxxxxxxxx 991 exercise hmmbuild @src/hmmbuild@ --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1001 exercise build/-h @src/hmmbuild@ -h 1011 exercise build/-n @src/hmmbuild@ -n foo --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1021 exercise build/-o @src/hmmbuild@ -o %HMMBUILD.out% --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1031 exercise build/-O @src/hmmbuild@ -O %HMMBUILD.sto% --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1041 exercise build/--amino @src/hmmbuild@ --amino --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1051 exercise build/--dna @src/hmmbuild@ --dna --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1061 exercise build/--rna @src/hmmbuild@ --rna --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/M1.sto! 1071 exercise build/--fast @src/hmmbuild@ --fast --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1081 exercise build/--hand @src/hmmbuild@ --hand --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1091 exercise build/--symfrac @src/hmmbuild@ --symfrac 1.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1101 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1111 exercise build/--wpb @src/hmmbuild@ --wpb --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1121 exercise build/--wgsc @src/hmmbuild@ --wgsc --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1131 exercise build/--wblosum @src/hmmbuild@ --wblosum --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1141 exercise build/--wnone @src/hmmbuild@ --wnone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 115# --wgiven not tested 1161 exercise build/--wid @src/hmmbuild@ --wblosum --wid 0.5 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1171 exercise build/--eent @src/hmmbuild@ --eent --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1181 exercise build/--eclust @src/hmmbuild@ --eclust --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1191 exercise build/--enone @src/hmmbuild@ --enone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1201 exercise build/--eset @src/hmmbuild@ --eset 1.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1211 exercise build/--ere @src/hmmbuild@ --eent --ere 0.55 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1221 exercise build/--esigma @src/hmmbuild@ --eent --esigma 44.0 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1231 exercise build/--eid @src/hmmbuild@ --eclust --eid 0.60 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1241 exercise build/--pnone @src/hmmbuild@ --pnone --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1251 exercise build/--plaplace @src/hmmbuild@ --plaplace --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1261 exercise build/--EmL @src/hmmbuild@ --EmL 100 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1271 exercise build/--EmN @src/hmmbuild@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1281 exercise build/--EvL @src/hmmbuild@ --EvL 100 --EmL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1291 exercise build/--EvN @src/hmmbuild@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1301 exercise build/--EfL @src/hmmbuild@ --EfL 100 --EmL 10 --EvL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1311 exercise build/--EfN @src/hmmbuild@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1321 exercise build/--Eft @src/hmmbuild@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1331 exercise build/--informat @src/hmmbuild@ --informat stockholm --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 1341 exercise build/--seed @src/hmmbuild@ --seed 42 --EmL 10 --EvL 10 --EfL 10 %HMMBUILD.hmm% !testsuite/20aa.sto! 135 136 137# hmmsearch xxxxxxxxxxxxxxxxxxxx 1381 prep rnddb @easel/miniapps/esl-shuffle@ -G --amino -L 100 -N 2 -o %RNDDB% 1391 exercise search @src/hmmsearch@ !tutorial/globins4.hmm! %RNDDB% 1401 exercise search/-h @src/hmmsearch@ -h 1411 exercise search/-o @src/hmmsearch@ -o %HMMSEARCH.out% !tutorial/globins4.hmm! %RNDDB% 1421 exercise search/-A @src/hmmsearch@ -A %HMMSEARCH.sto% !tutorial/globins4.hmm! %RNDDB% 1431 exercise search/--tblout @src/hmmsearch@ --tblout %HMMSEARCH.tbl% !tutorial/globins4.hmm! %RNDDB% 1441 exercise search/--domtblout @src/hmmsearch@ --domtblout %HMMSEARCH.dtbl% !tutorial/globins4.hmm! %RNDDB% 1451 exercise search/--pfamtblout @src/hmmsearch@ --pfamtblout %HMMSEARCH.dtbl% !tutorial/globins4.hmm! %RNDDB% 1461 exercise search/--acc @src/hmmsearch@ --acc !tutorial/globins4.hmm! %RNDDB% 1471 exercise search/--noali @src/hmmsearch@ --noali !tutorial/globins4.hmm! %RNDDB% 1481 exercise search/--notextw @src/hmmsearch@ --notextw !tutorial/globins4.hmm! %RNDDB% 1491 exercise search/--textw @src/hmmsearch@ --textw 256 !tutorial/globins4.hmm! %RNDDB% 1501 exercise search/-E @src/hmmsearch@ -E 0.01 !tutorial/globins4.hmm! %RNDDB% 1511 exercise search/-T @src/hmmsearch@ -T 20 !tutorial/globins4.hmm! %RNDDB% 1521 exercise search/--domE @src/hmmsearch@ --domE 0.01 !tutorial/globins4.hmm! %RNDDB% 1531 exercise search/--domT @src/hmmsearch@ --domT 20 !tutorial/globins4.hmm! %RNDDB% 1541 exercise search/--incE @src/hmmsearch@ --incE 0.01 !tutorial/globins4.hmm! %RNDDB% 1551 exercise search/--incT @src/hmmsearch@ --incT 20 !tutorial/globins4.hmm! %RNDDB% 1561 exercise search/--incdomE @src/hmmsearch@ --incdomE 0.01 !tutorial/globins4.hmm! %RNDDB% 1571 exercise search/--incdomT @src/hmmsearch@ --incdomT 20 !tutorial/globins4.hmm! %RNDDB% 1581 exercise search/--cut_ga @src/hmmsearch@ --cut_ga !tutorial/fn3.hmm! %RNDDB% 1591 exercise search/--cut_nc @src/hmmsearch@ --cut_nc !tutorial/fn3.hmm! %RNDDB% 1601 exercise search/--cut_tc @src/hmmsearch@ --cut_tc !tutorial/fn3.hmm! %RNDDB% 1611 exercise search/--max @src/hmmsearch@ --max !tutorial/globins4.hmm! %RNDDB% 1621 exercise search/--F1 @src/hmmsearch@ --F1 0.03 !tutorial/globins4.hmm! %RNDDB% 1631 exercise search/--F2 @src/hmmsearch@ --F2 0.002 !tutorial/globins4.hmm! %RNDDB% 1641 exercise search/--F3 @src/hmmsearch@ --F3 0.0002 !tutorial/globins4.hmm! %RNDDB% 1651 exercise search/--nobias @src/hmmsearch@ --nobias !tutorial/globins4.hmm! %RNDDB% 1661 exercise search/--nonull2 @src/hmmsearch@ --nonull2 !tutorial/globins4.hmm! %RNDDB% 1671 exercise search/-Z @src/hmmsearch@ -Z 45000000 !tutorial/globins4.hmm! %RNDDB% 1681 exercise search/--domZ @src/hmmsearch@ --domZ 45000000 !tutorial/globins4.hmm! %RNDDB% 1691 exercise search/--seed @src/hmmsearch@ --seed 42 !tutorial/globins4.hmm! %RNDDB% 1701 exercise search/--tformat @src/hmmsearch@ --tformat fasta !tutorial/globins4.hmm! %RNDDB% 171# --cpu: threads only 172# --mpi: MPI only 173 174# hmmscan xxxxxxxxxxxxxxxxxxxx 1751 exercise hmmscan @src/hmmscan@ %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1761 exercise scan/-h @src/hmmscan@ -h 1771 exercise scan/-o @src/hmmscan@ -o %SCAN.out% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1781 exercise scan/--tblout @src/hmmscan@ --tblout %SCAN.tbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1791 exercise scan/--domtblout @src/hmmscan@ --domtblout %SCAN.dtbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1801 exercise scan/--pfamtblout @src/hmmscan@ --pfamtblout %SCAN.ptbl% %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1811 exercise scan/--acc @src/hmmscan@ --acc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1821 exercise scan/--noali @src/hmmscan@ --noali %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1831 exercise scan/--notextw @src/hmmscan@ --notextw %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1841 exercise scan/--textw @src/hmmscan@ --textw 120 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1851 exercise scan/-E @src/hmmscan@ -E 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1861 exercise scan/-T @src/hmmscan@ -T 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1871 exercise scan/--domE @src/hmmscan@ --domE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1881 exercise scan/--domT @src/hmmscan@ --domT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1891 exercise scan/--incE @src/hmmscan@ --incE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1901 exercise scan/--incT @src/hmmscan@ --incT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1911 exercise scan/--incdomE @src/hmmscan@ --incdomE 0.01 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1921 exercise scan/--incdomT @src/hmmscan@ --incdomT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1931 exercise scan/--incdomT @src/hmmscan@ --incdomT 20 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1941 exercise scan/--cut_ga @src/hmmscan@ --cut_ga %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1951 exercise scan/--cut_nc @src/hmmscan@ --cut_nc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1961 exercise scan/--cut_tc @src/hmmscan@ --cut_tc %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1971 exercise scan/--max @src/hmmscan@ --max %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1981 exercise scan/--F1 @src/hmmscan@ --F1 0.03 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 1991 exercise scan/--F2 @src/hmmscan@ --F2 0.002 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2001 exercise scan/--F3 @src/hmmscan@ --F3 0.0002 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2011 exercise scan/--nobias @src/hmmscan@ --nobias %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2021 exercise scan/--nonull2 @src/hmmscan@ --nonull2 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2031 exercise scan/-Z @src/hmmscan@ -Z 45000000 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2041 exercise scan/--domZ @src/hmmscan@ --domZ 45000000 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2051 exercise scan/--seed @src/hmmscan@ --seed 42 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2061 exercise scan/--qformat @src/hmmscan@ --qformat fasta %MINIFAM.HMM% !tutorial/HBB_HUMAN! 2071 exercise scan/--cpu @src/hmmscan@ --cpu 2 %MINIFAM.HMM% !tutorial/HBB_HUMAN! 208 209 210# jackhmmer xxxxxxxxxxxxxxxxxxxx 2111 exercise jackhmmer @src/jackhmmer@ --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2121 exercise j/-h @src/jackhmmer@ -h 2131 exercise j/-N @src/jackhmmer@ -N 2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2141 exercise j/-o @src/jackhmmer@ -o %JHMMER.out% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2151 exercise j/-A @src/jackhmmer@ -A %JHMMER.sto% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2161 exercise j/--tblout @src/jackhmmer@ --tblout %JHMMER.tbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2171 exercise j/--domtblout @src/jackhmmer@ --domtblout %JHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2181 exercise j/--chkhmm @src/jackhmmer@ --chkhmm %JHMMER.ch% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2191 exercise j/--chkali @src/jackhmmer@ --chkali %JHMMER.ca% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2201 exercise j/--acc @src/jackhmmer@ --acc --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2211 exercise j/--noali @src/jackhmmer@ --noali --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2221 exercise j/--notextw @src/jackhmmer@ --notextw --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2231 exercise j/--textw @src/jackhmmer@ --textw 256 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2241 exercise j/--popen @src/jackhmmer@ --popen 0.4 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2251 exercise j/--pextend @src/jackhmmer@ --pextend 0.6 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2261 exercise j/--mxfile @src/jackhmmer@ --mxfile !easel/formats/BLOSUM62! --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2271 exercise j/-E @src/jackhmmer@ -E 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2281 exercise j/-T @src/jackhmmer@ -T 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2291 exercise j/--domE @src/jackhmmer@ --domE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2301 exercise j/--domT @src/jackhmmer@ --domT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2311 exercise j/--incE @src/jackhmmer@ --incE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2321 exercise j/--incT @src/jackhmmer@ --incT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2331 exercise j/--incdomE @src/jackhmmer@ --incdomE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2341 exercise j/--incdomT @src/jackhmmer@ --incdomT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2351 exercise j/--max @src/jackhmmer@ --max --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2361 exercise j/--F1 @src/jackhmmer@ --F1 0.03 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2371 exercise j/--F2 @src/jackhmmer@ --F2 0.002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2381 exercise j/--F3 @src/jackhmmer@ --F3 0.0002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2391 exercise j/--nobias @src/jackhmmer@ --nobias --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 240# builder options untested 2411 exercise j/--EmL @src/jackhmmer@ --EmL 100 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2421 exercise j/--EmN @src/jackhmmer@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2431 exercise j/--EvL @src/jackhmmer@ --EvL 100 --EmL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2441 exercise j/--EvN @src/jackhmmer@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2451 exercise j/--EfL @src/jackhmmer@ --EfL 100 --EmL 10 --EvL 10 !tutorial/HBB_HUMAN! %RNDDB% 2461 exercise j/--EfN @src/jackhmmer@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2471 exercise j/--Eft @src/jackhmmer@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2481 exercise j/--nonull2 @src/jackhmmer@ --nonull2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2491 exercise j/-Z @src/jackhmmer@ -Z 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2501 exercise j/--domZ @src/jackhmmer@ --domZ 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2511 exercise j/--seed @src/jackhmmer@ --seed 42 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2521 exercise j/--qformat @src/jackhmmer@ --qformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2531 exercise j/--tformat @src/jackhmmer@ --tformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 254# --cpu: threads only 255# --mpi: MPI only 2561 prep cleanup rm -f %JHMMER.ch%-1.hmm %JHMMER.ca%-1.sto 257 258 259# phmmer xxxxxxxxxxxxxxxxxxxx 2601 exercise phmmer @src/phmmer@ --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2611 exercise phmmer/-h @src/phmmer@ -h 2621 exercise phmmer/-o @src/phmmer@ -o %PHMMER.out% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2631 exercise phmmer/-A @src/phmmer@ -A %PHMMER.sto% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2641 exercise phmmer/--tblout @src/phmmer@ --tblout %PHMMER.tbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2651 exercise phmmer/--domtblout @src/phmmer@ --domtblout %PHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2661 exercise phmmer/--pfamtblout @src/phmmer@ --pfamtblout %PHMMER.dtbl% --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2671 exercise phmmer/--acc @src/phmmer@ --acc --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2681 exercise phmmer/--noali @src/phmmer@ --noali --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2691 exercise phmmer/--notextw @src/phmmer@ --notextw --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2701 exercise phmmer/--textw @src/phmmer@ --textw 256 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2711 exercise phmmer/--popen @src/phmmer@ --popen 0.4 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2721 exercise phmmer/--pextend @src/phmmer@ --pextend 0.6 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2731 exercise phmmer/--mxfile @src/phmmer@ --mxfile !easel/formats/BLOSUM62! --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2741 exercise phmmer/-E @src/phmmer@ -E 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2751 exercise phmmer/-T @src/phmmer@ -T 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2761 exercise phmmer/--domE @src/phmmer@ --domE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2771 exercise phmmer/--domT @src/phmmer@ --domT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2781 exercise phmmer/--incE @src/phmmer@ --incE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2791 exercise phmmer/--incT @src/phmmer@ --incT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2801 exercise phmmer/--incdomE @src/phmmer@ --incdomE 0.01 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2811 exercise phmmer/--incdomT @src/phmmer@ --incdomT 20 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2821 exercise phmmer/--max @src/phmmer@ --max --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2831 exercise phmmer/--F1 @src/phmmer@ --F1 0.03 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2841 exercise phmmer/--F2 @src/phmmer@ --F2 0.002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2851 exercise phmmer/--F3 @src/phmmer@ --F3 0.0002 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2861 exercise phmmer/--nobias @src/phmmer@ --nobias --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2871 exercise phmmer/--EmL @src/phmmer@ --EmL 100 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2881 exercise phmmer/--EmN @src/phmmer@ --EmN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2891 exercise phmmer/--EvL @src/phmmer@ --EvL 100 --EmL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2901 exercise phmmer/--EvN @src/phmmer@ --EvN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2911 exercise phmmer/--EfL @src/phmmer@ --EfL 100 --EmL 10 --EvL 10 !tutorial/HBB_HUMAN! %RNDDB% 2921 exercise phmmer/--EfN @src/phmmer@ --EfN 250 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2931 exercise phmmer/--Eft @src/phmmer@ --Eft 0.045 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2941 exercise phmmer/--nonull2 @src/phmmer@ --nonull2 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2951 exercise phmmer/-Z @src/phmmer@ -Z 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2961 exercise phmmer/--domZ @src/phmmer@ --domZ 45000000 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2971 exercise phmmer/--seed @src/phmmer@ --seed 42 --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2981 exercise phmmer/--qformat @src/phmmer@ --qformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 2991 exercise phmmer/--tformat @src/phmmer@ --tformat fasta --EmL 10 --EvL 10 --EfL 10 !tutorial/HBB_HUMAN! %RNDDB% 300# --cpu: threads only 301# --mpi: MPI only 302 303# nhmmer xxxxxxxxxxxxxxxxxxxx 3041 prep rnddb @easel/miniapps/esl-shuffle@ -G --dna -L 10000 -N 2 -o %RNDDB% 3051 exercise nhmmer @src/nhmmer@ !tutorial/MADE1.hmm! %RNDDB% 3061 exercise nhmmer/-h @src/nhmmer@ -h 3071 exercise nhmmer/-o @src/nhmmer@ -o %nhmmer.out% !tutorial/MADE1.hmm! %RNDDB% 3081 exercise nhmmer/-A @src/nhmmer@ -A %nhmmer.sto% !tutorial/MADE1.hmm! %RNDDB% 3091 exercise nhmmer/--tblout @src/nhmmer@ --tblout %nhmmer.tbl% !tutorial/MADE1.hmm! %RNDDB% 3101 exercise nhmmer/--dfamtblout @src/nhmmer@ --dfamtblout %nhmmer.dtbl% !tutorial/MADE1.hmm! %RNDDB% 3111 exercise nhmmer/--acc @src/nhmmer@ --acc !tutorial/MADE1.hmm! %RNDDB% 3121 exercise nhmmer/--noali @src/nhmmer@ --noali !tutorial/MADE1.hmm! %RNDDB% 3131 exercise nhmmer/--notextw @src/nhmmer@ --notextw !tutorial/MADE1.hmm! %RNDDB% 3141 exercise nhmmer/--textw @src/nhmmer@ --textw 256 !tutorial/MADE1.hmm! %RNDDB% 3151 exercise nhmmer/-E @src/nhmmer@ -E 0.01 !tutorial/MADE1.hmm! %RNDDB% 3161 exercise nhmmer/-T @src/nhmmer@ -T 20 !tutorial/MADE1.hmm! %RNDDB% 3171 exercise nhmmer/--incE @src/nhmmer@ --incE 0.01 !tutorial/MADE1.hmm! %RNDDB% 3181 exercise nhmmer/--incT @src/nhmmer@ --incT 20 !tutorial/MADE1.hmm! %RNDDB% 3191 exercise nhmmer/--max @src/nhmmer@ --max !tutorial/MADE1.hmm! %RNDDB% 3201 exercise nhmmer/--F1 @src/nhmmer@ --F1 0.03 !tutorial/MADE1.hmm! %RNDDB% 3211 exercise nhmmer/--F2 @src/nhmmer@ --F2 0.002 !tutorial/MADE1.hmm! %RNDDB% 3221 exercise nhmmer/--F3 @src/nhmmer@ --F3 0.0002 !tutorial/MADE1.hmm! %RNDDB% 3231 exercise nhmmer/--nobias @src/nhmmer@ --nobias !tutorial/MADE1.hmm! %RNDDB% 3241 exercise nhmmer/--nonull2 @src/nhmmer@ --nonull2 !tutorial/MADE1.hmm! %RNDDB% 3251 exercise nhmmer/-Z @src/nhmmer@ -Z 45000000 !tutorial/MADE1.hmm! %RNDDB% 3261 exercise nhmmer/--seed @src/nhmmer@ --seed 42 !tutorial/MADE1.hmm! %RNDDB% 327 328 329# nhmmscan xxxxxxxxxxxxxxxxxxxx 3301 prep rnddb @easel/miniapps/esl-shuffle@ -G --dna -L 10000 -N 2 -o %RNDDB% 3311 prep press @src/hmmpress@ -f !tutorial/MADE1.hmm! 3321 exercise nhmmscan @src/nhmmscan@ !tutorial/MADE1.hmm! %RNDDB% 3331 exercise nhmmscan/-h @src/nhmmscan@ -h 3341 exercise nhmmscan/-o @src/nhmmscan@ -o %nhmmscan.out% !tutorial/MADE1.hmm! %RNDDB% 3351 exercise nhmmscan/--tblout @src/nhmmscan@ --tblout %nhmmscan.tbl% !tutorial/MADE1.hmm! %RNDDB% 3361 exercise nhmmscan/--dfamtblout @src/nhmmscan@ --dfamtblout %nhmmscan.dtbl% !tutorial/MADE1.hmm! %RNDDB% 3371 exercise nhmmscan/--acc @src/nhmmscan@ --acc !tutorial/MADE1.hmm! %RNDDB% 3381 exercise nhmmscan/--noali @src/nhmmscan@ --noali !tutorial/MADE1.hmm! %RNDDB% 3391 exercise nhmmscan/--notextw @src/nhmmscan@ --notextw !tutorial/MADE1.hmm! %RNDDB% 3401 exercise nhmmscan/--textw @src/nhmmscan@ --textw 256 !tutorial/MADE1.hmm! %RNDDB% 3411 exercise nhmmscan/-E @src/nhmmscan@ -E 0.01 !tutorial/MADE1.hmm! %RNDDB% 3421 exercise nhmmscan/-T @src/nhmmscan@ -T 20 !tutorial/MADE1.hmm! %RNDDB% 3431 exercise nhmmscan/--incE @src/nhmmscan@ --incE 0.01 !tutorial/MADE1.hmm! %RNDDB% 3441 exercise nhmmscan/--incT @src/nhmmscan@ --incT 20 !tutorial/MADE1.hmm! %RNDDB% 3451 exercise nhmmscan/--max @src/nhmmscan@ --max !tutorial/MADE1.hmm! %RNDDB% 3461 exercise nhmmscan/--F1 @src/nhmmscan@ --F1 0.03 !tutorial/MADE1.hmm! %RNDDB% 3471 exercise nhmmscan/--F2 @src/nhmmscan@ --F2 0.002 !tutorial/MADE1.hmm! %RNDDB% 3481 exercise nhmmscan/--F3 @src/nhmmscan@ --F3 0.0002 !tutorial/MADE1.hmm! %RNDDB% 3491 exercise nhmmscan/--nobias @src/nhmmscan@ --nobias !tutorial/MADE1.hmm! %RNDDB% 3501 exercise nhmmscan/--nonull2 @src/nhmmscan@ --nonull2 !tutorial/MADE1.hmm! %RNDDB% 3511 exercise nhmmscan/-Z @src/nhmmscan@ -Z 45000000 !tutorial/MADE1.hmm! %RNDDB% 3521 exercise nhmmscan/--seed @src/nhmmscan@ --seed 42 !tutorial/MADE1.hmm! %RNDDB% 3531 prep cleanup rm !tutorial/MADE1.hmm!.h3? 354 355# hmmemit xxxxxxxxxxxxxxxxxxxx 3561 exercise hmmemit @src/hmmemit@ !testsuite/Caudal_act.hmm! 3571 exercise hmmemit/-h @src/hmmemit@ -h 3581 exercise hmmemit/-c @src/hmmemit@ -c !testsuite/Caudal_act.hmm! 3591 exercise hmmemit/-o @src/hmmemit@ -o /dev/null !testsuite/Caudal_act.hmm! 3601 exercise hmmemit/-p @src/hmmemit@ -p !testsuite/Caudal_act.hmm! 3611 exercise hmmemit/-N @src/hmmemit@ -N 10 !testsuite/Caudal_act.hmm! 3621 exercise hmmemit/-L @src/hmmemit@ -p -L 50 !testsuite/Caudal_act.hmm! 3631 exercise hmmemit/--local @src/hmmemit@ -p --local !testsuite/Caudal_act.hmm! 3641 exercise hmmemit/--unilocal @src/hmmemit@ -p --unilocal !testsuite/Caudal_act.hmm! 3651 exercise hmmemit/--glocal @src/hmmemit@ -p --glocal !testsuite/Caudal_act.hmm! 3661 exercise hmmemit/--uniglocal @src/hmmemit@ -p --uniglocal !testsuite/Caudal_act.hmm! 367 368# xxxxxxxxx xxxxxxxxxxxxxxxxxxxx 3691 exercise hmmfetch @src/hmmfetch@ %MINIFAM.HMM% Caudal_act 3701 exercise hmmstat @src/hmmstat@ !testsuite/Caudal_act.hmm! 3711 exercise hmmlogo @src/hmmlogo@ !testsuite/Caudal_act.hmm! 3721 exercise hmmconvert @src/hmmconvert@ !testsuite/Caudal_act.hmm! 3731 exercise hmmsim @src/hmmsim@ !testsuite/Caudal_act.hmm! 374 375################################################################# 376# Integration tests 377################################################################ 378 379# Run-to-run variation tests 380# By default, stochastic simulations are seeded reproducibly, so there 381# is no run-to-run variation; whereas with different RNG seeds, 382# run-to-run variation does occur. [xref J5/99] 383# The hmmemit seed of 35 is carefully chosen to generate a target sequence 384# that requires stochastic clustering when aligned to the Caudal_act.hmm test 385# To search for new seeds, the command line is something like: 386# ( ../src/hmmemit --seed 35 -p Caudal_act.hmm | ../src/hmmsearch --seed 2 --tblout foo.out Caudal_act.hmm - > /dev/null ; cat foo.out ) 387# looking for high scoring sequences that force a stochastic clustering step. 388# 389# xxxxxxxxxxxxxxxxxxxx 3901 prep seq @src/hmmemit@ --seed 35 -p %CAUDAL.HMM% > %TESTSEQ% 3911 prep db_1 @src/hmmemit@ --seed 35 -p %CAUDAL.HMM% > %TESTDB% 3921 prep db_2 @easel/miniapps/esl-reformat@ fasta !testsuite/Caudal_act.sto! >> %TESTDB% 3931 prep db_3 @easel/miniapps/esl-shuffle@ -G --amino -N 100 -L 350 >> %TESTDB% 3941 exercise hmmbuild_variation !testsuite/i1-build-variation.sh! @src/hmmbuild@ !testsuite/Caudal_act.sto! %OUTFILES% 3951 exercise hmmscan_variation !testsuite/i2-search-variation.sh! @src/hmmscan@ %MINIFAM.HMM% %TESTSEQ% %OUTFILES% 3961 exercise hmmsearch_variation !testsuite/i2-search-variation.sh! @src/hmmsearch@ %CAUDAL.HMM% %TESTDB% %OUTFILES% 3971 exercise phmmer_variation !testsuite/i3-seqsearch-variation.sh! @src/phmmer@ %OUTFILES% 3983 exercise jackhmmer_variation !testsuite/i3-seqsearch-variation.sh! @src/jackhmmer@ %OUTFILES% 3991 exercise mapali !testsuite/i6-hmmalign-mapali.pl! @src/hmmalign@ @easel/miniapps/esl-reformat@ !testsuite! %OUTFILES% 4001 exercise fragments !testsuite/i7-hmmbuild-fragments.pl! @src/hmmbuild@ %OUTFILES% 4011 exercise nonresidues !testsuite/i8-nonresidues.pl! @@ !! %OUTFILES% 4021 exercise opt-annotation !testsuite/i9-optional-annotation.pl! @@ !! %OUTFILES% 4031 exercise dup-names !testsuite/i10-duplicate-names.pl! @@ !! %OUTFILES% 4041 exercise mapali-again !testsuite/i11-hmmalign-mapali.pl! @@ !! %OUTFILES% 4051 exercise delete-corruption !testsuite/i12-delete-corruption.pl! @@ !! %OUTFILES% 4061 exercise msa-integrity !testsuite/i13-msa-integrity.pl! @@ !! %OUTFILES% 4071 exercise hmmemit-consensus !testsuite/i14-hmmemit-consensus.pl! @@ !! %OUTFILES% 4081 exercise hmmconvert !testsuite/i15-hmmconvert.pl! @@ !! %OUTFILES% 4091 exercise stdin_pipes !testsuite/i17-stdin.pl! @@ !! %OUTFILES% 4101 exercise nhmmer_generic !testsuite/i18-nhmmer-generic.pl! @@ !! %OUTFILES% 4111 exercise hmmpgmd_ga !testsuite/i19-hmmpgmd-ga.pl! @@ !! %OUTFILES% 412#comment out fmindex test until it's been returned to life 413#1 exercise fmindex-core !testsuite/i20-fmindex-core.pl! @@ !! %OUTFILES% 4141 exercise rewind !testsuite/i21-rewind.pl! @@ !! %OUTFILES% 4151 exercise hmmpgmd_shard_ga !testsuite/i22-hmmpgmd-shard-ga.pl! @@ !! %OUTFILES% 4161 exercise bad-fasta !testsuite/i23-bad-fasta.sh! @@ !! %OUTFILES% 4171 exercise brute-itest @src/itest_brute@ 4181 exercise hmmpress-itest !src/hmmpress.itest.pl! @src/hmmpress@ %MINIFAM.HMM% %TMPPFX% 419 420################################################################ 421# Fixed bug tests 422################################################################ 423 424# xxxxxxxxxxxxxxxxxxxx 4251 exercise h39 @src/hmmsearch@ !testsuite/M1.hmm! !testsuite/M1.sto! 4261 exercise h45 !testsuite/i4-zerolength-seqs.sh! @@ !! %MINIFAM.HMM% %OUTFILES% 4271 exercise h50 !testsuite/i5-hmmbuild-naming.pl! @@ !! %OUTFILES% 4281 exercise h82 !testsuite/i16-build-allins.pl! @@ !! %OUTFILES% 4291 exercise iss159 !testsuite/iss159-nhmmer-overlap.py! @@ !! %OUTFILES% 430 431################################################################ 432# valgrind tests (optional. 'make SQCLEVEL=3 check') 433################################################################ 434 435# xxxxxxxxxxxxxxxxxxxx 4363 valgrind hmmer @src/hmmer_utest@ 4373 valgrind build @src/build_utest@ 4383 valgrind generic_fwdback @src/generic_fwdback_utest@ 4393 valgrind generic_msv @src/generic_msv_utest@ 4403 valgrind generic_stotrace @src/generic_stotrace_utest@ 4413 valgrind generic_viterbi @src/generic_viterbi_utest@ 4423 valgrind logsum @src/logsum_utest@ 4433 valgrind modelconfig @src/modelconfig_utest@ 4443 valgrind p7_alidisplay @src/p7_alidisplay_utest@ 4453 valgrind p7_bg @src/p7_bg_utest@ 4463 valgrind p7_gmx @src/p7_gmx_utest@ 4473 valgrind p7_hmm @src/p7_hmm_utest@ 4483 valgrind p7_hmmfile @src/p7_hmmfile_utest@ 4493 valgrind p7_profile @src/p7_profile_utest@ 4503 valgrind p7_tophits @src/p7_tophits_utest@ 4513 valgrind p7_trace @src/p7_trace_utest@ 452 4533 valgrind decoding @src/impl/decoding_utest@ 4543 valgrind fwdback @src/impl/fwdback_utest@ 4553 valgrind io @src/impl/io_utest@ 4563 valgrind msvfilter @src/impl/msvfilter_utest@ 4573 valgrind null2 @src/impl/null2_utest@ 4583 valgrind optacc @src/impl/optacc_utest@ 4593 valgrind stotrace @src/impl/stotrace_utest@ 4603 valgrind vitfilter @src/impl/vitfilter_utest@ 461 4621 prep minifam @src/hmmbuild@ %MINIFAM.HMM% !testsuite/minifam! 463 4643 valgrind hmmbuild @src/hmmbuild@ %GLOBIN.HMM% !tutorial/globins4.sto! 4653 valgrind hmmconvert @src/hmmconvert@ -b %GLOBIN.HMM% 4663 valgrind hmmalign @src/hmmalign@ %GLOBIN.HMM% !tutorial/globins45.fa! 4673 valgrind hmmemit @src/hmmemit@ -N10 %GLOBIN.HMM% 4683 valgrind hmmpress @src/hmmpress@ -f %MINIFAM.HMM% 4693 valgrind hmmfetch @src/hmmfetch@ %MINIFAM.HMM% Caudal_act 4703 valgrind hmmscan @src/hmmscan@ %MINIFAM.HMM% !tutorial/HBB_HUMAN! 4713 valgrind hmmsearch @src/hmmsearch@ %GLOBIN.HMM% !tutorial/globins45.fa! 4723 valgrind hmmsim @src/hmmsim@ %GLOBIN.HMM% 4733 valgrind hmmstat @src/hmmstat@ %MINIFAM.HMM% 4743 valgrind jackhmmer @src/jackhmmer@ !tutorial/HBB_HUMAN! !tutorial/globins45.fa! 4753 valgrind phmmer @src/phmmer@ !tutorial/HBB_HUMAN! !tutorial/globins45.fa! 476 477# some derivatives of tmpfiles created by hmmpress, not sqc itself: clean up 4781 prep minifam rm -f %MINIFAM.HMM%.h3f %MINIFAM.HMM%.h3p %MINIFAM.HMM%.h3m %MINIFAM.HMM%.h3i 479 480 481