bam2bcf_indel tidyups.

- Remove STRBZ and BQBZ as unuseful stats.

- Only compute stats once per indel rather than per type.

- Replace some pointless mallocs with fixed arrays as the maximum
  number of types was already hard-coded.

- General code tidyups

bam2bcf.c

@@ -64,8 +64,6 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
     bca->ialt_mq = (int*) malloc(bca->nqual*sizeof(int));
     bca->ref_bq  = (int*) malloc(bca->nqual*sizeof(int));
     bca->alt_bq  = (int*) malloc(bca->nqual*sizeof(int));
-    bca->iref_bq = (int*) malloc(bca->nqual*sizeof(int));
-    bca->ialt_bq = (int*) malloc(bca->nqual*sizeof(int));
     bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int));
     bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int));
     return bca;
@@ -83,7 +81,6 @@ void bcf_call_destroy(bcf_callaux_t *bca)
     free(bca->ref_mq); free(bca->alt_mq);
     free(bca->iref_mq); free(bca->ialt_mq);
     free(bca->ref_bq); free(bca->alt_bq);
-    free(bca->iref_bq); free(bca->ialt_bq);
     free(bca->fwd_mqs); free(bca->rev_mqs);
     bca->nqual = 0;
     free(bca->bases); free(bca->inscns); free(bca);
@@ -162,8 +159,6 @@ void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call)
     memset(bca->ialt_mq,0,sizeof(int)*bca->nqual);
     memset(bca->ref_bq,0,sizeof(int)*bca->nqual);
     memset(bca->alt_bq,0,sizeof(int)*bca->nqual);
-    memset(bca->iref_bq,0,sizeof(int)*bca->nqual);
-    memset(bca->ialt_bq,0,sizeof(int)*bca->nqual);
     memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual);
     memset(bca->rev_mqs,0,sizeof(int)*bca->nqual);
     if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
@@ -174,8 +169,6 @@ void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call)
     memset(bca->alt_scl,  0, 100*sizeof(int));
     memset(bca->iref_scl, 0, 100*sizeof(int));
     memset(bca->ialt_scl, 0, 100*sizeof(int));
-    memset(bca->iref_str, 0, 100*sizeof(int));
-    memset(bca->ialt_str, 0, 100*sizeof(int));
 }
 
 /*
@@ -885,13 +878,9 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int
                                            bca->npos, 0, 1);
         call->mwu_mq  = calc_mwu_biasZ(bca->iref_mq,  bca->ialt_mq,
                                        bca->nqual,1,1);
-        call->mwu_bq  = calc_mwu_biasZ(bca->iref_bq,  bca->ialt_bq,
-                                       bca->nqual,0,1);
         if ( bca->fmt_flag & B2B_INFO_SCB )
             call->mwu_sc  = calc_mwu_biasZ(bca->iref_scl, bca->ialt_scl,
                                            100, 0,1);
-        call->mwu_str  = calc_mwu_biasZ(bca->iref_str,  bca->ialt_str,
-                                        100,0,1);
     } else {
         if (bca->fmt_flag & B2B_INFO_RPB)
             call->mwu_pos = calc_mwu_biasZ(bca->ref_pos, bca->alt_pos,
@@ -905,7 +894,6 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int
         if ( bca->fmt_flag & B2B_INFO_SCB )
             call->mwu_sc  = calc_mwu_biasZ(bca->ref_scl, bca->alt_scl,
                                            100, 0,1);
-        call->mwu_str = HUGE_VAL;
     }
 
 
@@ -1025,7 +1013,6 @@ int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag,
     if ( bc->mwu_mqs != HUGE_VAL )  bcf_update_info_float(hdr, rec, "MQSBZ", &bc->mwu_mqs, 1);
     if ( bc->mwu_bq != HUGE_VAL )   bcf_update_info_float(hdr, rec, "BQBZ", &bc->mwu_bq, 1);
     if ( bc->mwu_sc != HUGE_VAL )   bcf_update_info_float(hdr, rec, "SCBZ", &bc->mwu_sc, 1);
-    if ( bc->mwu_str != HUGE_VAL )   bcf_update_info_float(hdr, rec, "STRBZ", &bc->mwu_str, 1);
 #else
     if ( bc->mwu_pos != HUGE_VAL )  bcf_update_info_float(hdr, rec, "RPB", &bc->mwu_pos, 1);
     if ( bc->mwu_mq != HUGE_VAL )   bcf_update_info_float(hdr, rec, "MQB", &bc->mwu_mq, 1);

bam2bcf.h

@@ -91,10 +91,9 @@ typedef struct __bcf_callaux_t {
     float max_frac; // for collecting indel candidates
     int per_sample_flt; // indel filtering strategy
     int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests
-    int *iref_pos, *ialt_pos, *iref_mq, *ialt_mq, *iref_bq, *ialt_bq; // for indels
+    int *iref_pos, *ialt_pos, *iref_mq, *ialt_mq; // for indels
     int ref_scl[100], alt_scl[100];   // soft-clip length bias; SNP
     int iref_scl[100], ialt_scl[100]; // soft-clip length bias; INDEL
-    int iref_str[100], ialt_str[100]; // STR score bias; INDEL
     // for internal uses
     int max_bases;
     int indel_types[4];     // indel lengths
@@ -141,7 +140,7 @@ typedef struct {
     int32_t *PL, *DP4, *ADR, *ADF, *SCR, *QS;
     uint8_t *fmt_arr;
     float vdb; // variant distance bias
-    float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc, mwu_str;
+    float mwu_pos, mwu_mq, mwu_bq, mwu_mqs, mwu_sc;
 #if CDF_MWU_TESTS
     float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf;
 #endif