Fixes recently introduced minor memory leak in hmmonly pipeline (cm_p…

…ipeline.c) revealed by Valgrind. Removes debugging print statements related to new clan options (cmscan.c). Adds two files used by testsuite for new overlap/clan option testing.

src/cm_pipeline.c

@@ -1527,11 +1527,11 @@ cm_Pipeline(CM_PIPELINE *pli, off_t cm_offset, P7_OPROFILE *om, P7_BG *bg, float
           if((status = pli_p7_env_def(pli, om, bg, p7_evparam, sq2search, ws, we, nwin, opt_hmm, opt_gm, opt_Rgm, opt_Lgm, opt_Tgm, &(p7esAA[p]), &(p7eeAA[p]), &(p7ebAA[p]), &(np7envA[p]))) != eslOK) return status;
         } 
       } /* end of if(pli->do_edef) */         
-      if(ws    != NULL) { free(ws);    ws   = NULL; }
-      if(we    != NULL) { free(we);    we   = NULL; }
-      if(wb    != NULL) { free(wb);    wb   = NULL; }
-      nwin = 0;
-    }
+    } /* end of 'else' entered if p != PLI_PASS_HMM_ONLY_ANY */
+    if(ws    != NULL) { free(ws);    ws   = NULL; }
+    if(we    != NULL) { free(we);    we   = NULL; }
+    if(wb    != NULL) { free(wb);    wb   = NULL; }
+    nwin = 0;
   } /* end of 'for(p = PLI_PASS_STD_ANY; p <= PLI_NPASSES; p++)', first loop over pipeline passes */
   
   if(pli->do_one_cmpass) { 

src/cmscan.c

@@ -2630,16 +2630,6 @@ read_clan_info_file(char *filename, char *errbuf, CM_FILE *cmfp, ESL_KEYHASH **r
 
   if(nclan == 0) ESL_FAIL(status, errbuf, "Error reading %s, no clans present in file\n", filename);
 
-  /* debug print */
-  for(i = 0; i < nclan; i++) { 
-    printf("clan %d %s\n", i, esl_keyhash_Get(clan_name_kh, i));
-  }
-  printf("\n\n");
-  for(i = 0; i < nfam; i++) { 
-    printf("fam %d %s clan: %d\n", i, esl_keyhash_Get(clan_fam_kh, i), clan_mapA[i]);
-  }
-  printf("\n\n");
-
   *ret_clan_name_kh = clan_name_kh;
   *ret_clan_fam_kh  = clan_fam_kh;
   *ret_clan_mapA    = clan_mapA;

testsuite/5.claninfo

@@ -0,0 +1 @@
+CL00001 tRNA tRNA-Sec

testsuite/Rfam.12.1.clanin

@@ -0,0 +1,104 @@
+CL00001 tRNA cyano_tmRNA tRNA-Sec mt-tmRNA
+CL00003 Metazoa_SRP Bacteria_small_SRP Fungi_SRP Dictyostelium_SRP Bacteria_large_SRP Plant_SRP Protozoa_SRP Archaea_SRP
+CL00004 Telomerase-cil
+CL00008 U54 snoU54
+CL00010 Hammerhead_3 Hammerhead_1 Hammerhead_HH9 Hammerhead_II Hammerhead_HH10
+CL00011 GlmZ_SraJ GlmY_tke1
+CL00012 SAM SAM-IV
+CL00013 7SK Arthropod_7SK
+CL00014 CRISPR-DR2 CRISPR-DR4 CRISPR-DR14 CRISPR-DR17 CRISPR-DR25 CRISPR-DR43 CRISPR-DR66
+CL00015 CRISPR-DR5 CRISPR-DR7 CRISPR-DR63 CRISPR-DR64
+CL00016 FinP traJ_5
+CL00017 IRES_HCV IRES_Pesti
+CL00018 SCARNA24 SCARNA3
+CL00019 SCARNA4 SCARNA15
+CL00021 SNORA16 SNORA2 snopsi28S-3327 snR189 snR46 S_pombe_snR46
+CL00022 SNORA3 snR11
+CL00023 SNORA4 snR83
+CL00024 SNORA5 snR85
+CL00025 SNORA7 snR81
+CL00026 SNORA8 snR31
+CL00027 SNORA9 snR33 snR43 S_pombe_snR33
+CL00028 SNORA13 snR35 S_pombe_snR35
+CL00029 SNORA43 SNORA17
+CL00030 SNORA20 SNORA29
+CL00031 SNORA21 snR10 S_pombe_snR10
+CL00032 SNORA27 SNORA26 snR42 S_pombe_snR42
+CL00033 SNORA28 snopsi18S-841 snR80
+CL00034 SNORA50 SNORA54 SNORA35 SNORA76
+CL00035 SNORA36 snR36 snR44 S_pombe_snR36
+CL00036 SNORA44 SNORA58 snR161 snR9
+CL00037 SNORA48 snR86
+CL00038 SNORA66 snoR98 SNORA52 SNORA18 snoR80 snR49 snR5 S_pombe_snR5
+CL00039 SNORA56 snR8
+CL00040 SNORA62 snR3 snR82 S_pombe_snR3
+CL00041 SNORA64 snR37
+CL00042 SNORA65 snR34 snoR2
+CL00043 SNORA74 snR191
+CL00044 SNORD12 snR190
+CL00045 SNORD15 snR75 snR13 snoZ5
+CL00046 SNORD16 snR87
+CL00047 SNORD18 snoU18
+CL00048 SNORD19 SNORD19B
+CL00049 SNORD25 snR56
+CL00050 SNORD26 SNORD81
+CL00051 SNORD36 SNORD29 snoZ223 SNORD38 snosnR69 snosnR61 snosnR71 SNORD78 snoR69Y snR47 snoU36a
+CL00052 SNORD30 snoU30
+CL00053 SNORD31 snoZ17 snR67 snoR35
+CL00054 SNORD33 snoZ196 SNORD51 snosnR55 snoMe18S-Um1356 snoMe28S-Am982 snR39 snR40
+CL00055 SNORD34 snR62
+CL00056 SNORD35 snoZ161_228 snR73
+CL00057 SNORD39 snoZ7 snoZ101 SNORD65 snoR77Y snR77
+CL00058 SNORD57 SNORD41 snR51
+CL00059 SNORD43 snR70
+CL00060 SNORD44 snoZ102_R77
+CL00061 SNORD46 snR63
+CL00062 SNORD49 snoZ112 snoU49
+CL00063 SNORD52 SNORD53_SNORD92 snoZ157 snR78
+CL00064 SNORD58 SNORD99
+CL00065 snoZ159 SNORD59 snosnR54
+CL00066 SNORD60 snoR1 snosnR48 snoMe28S-G3255 sn2903
+CL00067 SNORD61 snoU61 SNORD125
+CL00068 SNORD62 snoR41 snR41
+CL00069 SNORD79 SNORD113 SNORD74 snoR44_J54 snosnR64 snoMe28S-Cm2645 SNORD64 SNORD112 SNORD109A
+CL00070 snosnR60_Z15 SNORD77 Afu_263
+CL00071 SNORD88 snR76 snoR118
+CL00072 SNORD96 SNORD2
+CL00073 snoR30 SNORD100
+CL00074 SNORD101 snoR60
+CL00075 SNORD105 snoU105B
+CL00076 SNORD110 snoR14
+CL00077 SNORND104 snR58
+CL00078 SNORA73 snR30
+CL00079 snR68 snoR27
+CL00080 snoR53 snoR53Y
+CL00081 snoZ279_R105_R108 snoU13
+CL00082 snoU89 snoU85
+CL00083 mir-6 mir-11
+CL00084 mir-3 mir-318
+CL00085 mir-16 mir-15
+CL00086 mir-28 mir-708
+CL00087 mir-34 mir-449
+CL00088 mir-36 mir-42 mir-35
+CL00089 mir-190 mir-50
+CL00090 mir-74 mir-73
+CL00091 bantam mir-81
+CL00092 mir-137 mir-234
+CL00093 mir-183 mir-182 mir-263 mir-228
+CL00094 mir-216 mir-283
+CL00095 mir-279 mir-996
+CL00096 mir-515 mir-290 mir-302 miR-430
+CL00097 mir-BART1 mir-BART3
+CL00098 MIR169_2 MIR169_5
+CL00099 MIR171_1 MIR171_2
+CL00100 U3 Fungi_U3 Plant_U3 ACEA_U3
+CL00101 Cobalamin
+CL00102 group-II-D1D4-1 group-II-D1D4-2 group-II-D1D4-3 group-II-D1D4-4 group-II-D1D4-5 group-II-D1D4-6 group-II-D1D4-7
+CL00103 SNORD11 SNORD11B
+CL00104 HBV_epsilon AHBV_epsilon
+CL00105 SraC_RyeA RyeB
+CL00106 CsrB CsrC PrrB_RsmZ RsmY TwoAYGGAY rsmX
+CL00108 suhB
+CL00110 mir-19 mir-363
+CL00111 SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia
+CL00112 LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya