[feat, fix] Fix qscore bins add 0.499

[fix]

Fix memleak with simulating with depth = inf

Fix qscore calculation, add +0.499. Update test cases expected results.

[feat]

Improve poisson sampler

Add own implementation of beta sampler

Add -printBasePickError -printGlError -printQsError -printQScore options

Add make test-% for detailed tests like vg or all

Add gtDiscordance misc program updated version

Change version to 0.4.3

Makefile

@@ -204,7 +204,7 @@ FLAGS := $(CPPFLAGS) $(CXXFLAGS)
 
 
 # Versioning
-VERSION = v0.4.1
+VERSION = v0.4.3
 
 ifneq ($(wildcard .git),)
 VERSION := $(VERSION)-$(shell git describe --always)
@@ -267,10 +267,13 @@ clean:
 ## [test]
 # - run unit tests
 
-.PHONY: test
+.PHONY: test test-%
 test:
 	bash test/runTests.sh
 
+test-%:
+	bash test/runTests.sh $*
+
 ####################################################################################################
 ## [.activate_module]
 

bcf_utils.cpp

@@ -205,18 +205,9 @@ simRecord::simRecord(bcf_hdr_t* in_hdr) {
 
     this->set_hdr(in_hdr);
 
-    if (args->mps_depths_fn != NULL) {
-        this->mps_depths = read_depthsFile(args->mps_depths_fn, this->nSamples);
-
-        fprintf(stderr, "\n");
-        if (args->verbose > 0) {
-            for (int s = 0; s < this->nSamples; s++) {
-                fprintf(stderr,
-                    "Individual \'%s\' (index:%d) mean per-site depth is "
-                    "set to %f\n",
-                    bcf_hdr_int2id(this->hdr, BCF_DT_SAMPLE, s),
-                    s, this->mps_depths[s]);
-            }
+    if (args->mps_depths != NULL) {
+        if (args->n_mps_depths != this->nSamples) {
+            ERROR("Number of depths provided in the depths file (%d) does not match the number of samples (%d) in the input VCF file.", args->n_mps_depths, this->nSamples);
         }
     }
 
@@ -410,11 +401,6 @@ simRecord::~simRecord() {
     free(this->current_size_bcf_tag_number);
     this->current_size_bcf_tag_number = NULL;
 
-    if (NULL != this->mps_depths) {
-        free(this->mps_depths);
-        this->mps_depths = NULL;
-    }
-
     free(this->alleles2acgt);
     this->alleles2acgt = NULL;
     free(this->acgt2alleles);

bcf_utils.h

@@ -117,8 +117,6 @@ typedef struct simRecord {
     // current sizes in use for enum INFO/FORMAT<Number=bcf_tag_number>
     int* current_size_bcf_tag_number = NULL;
 
-    double* mps_depths = NULL;
-
     // ---
     // always created, only added if addTYPE==1
     int32_t* fmt_dp_arr = NULL;

gl_methods.cpp

@@ -184,8 +184,8 @@ void alleles_calculate_gls_log10_glModel2_precise1(simRecord* sim) {
 
                 bo = sim->bases[s][read_i];
 
-
                 e = sim->base_error_probs[s][read_i];
+
                 if (0.0 == e) {
                     homT = 0.0;
                     het = -0.30103;