Improvements to indel calling.

INSTALL

@@ -266,3 +266,22 @@ mingw-w64-x86_64-tools-git
 
 (The last is only needed for building libraries compatible with MSVC.)
 
+Windows MSYS2/MINGW64
+---------------------
+
+The configure script must be used as without it the compilation will
+likely fail.
+
+Follow MSYS2 installation instructions at
+https://www.msys2.org/wiki/MSYS2-installation/
+
+Then relaunch to MSYS2 shell using the "MSYS2 MinGW x64" executable.
+Once in that environment (check $MSYSTEM equals "MINGW64") install the
+compilers using pacman -S and the following package list:
+
+base-devel mingw-w64-x86_64-toolchain
+mingw-w64-x86_64-libdeflate mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2
+mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
+mingw-w64-x86_64-tools-git
+
+(The last is only needed for building libraries compatible with MSVC.)

bam2bcf.c

@@ -234,11 +234,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                 // particularly indicative of being a good REF match either,
                 // at least not in low coverage.  So require solid coverage
                 // before we start utilising such quals.
-                b = 0;
+                if (b != 0)
+                    b = 5;
                 q = (int)bam_get_qual(p->b)[p->qpos];
                 seqQ = (3*seqQ + 2*q)/8;
             }
             if (_n > 20 && seqQ > 40) seqQ = 40;
+            // Note baseQ changes some output fields such as I16, but has no
+            // significant affect on "call".
             baseQ  = p->aux>>8&0xff;
 
             is_diff = (b != 0);
@@ -357,9 +360,19 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
             for (i=0; i<4; i++) r->ADF[i] += lroundf((float)dp_ambig * r->ADF[i]/dp);
     }
 
+    // Else consider downgrading bca->bases[] scores by AD vs AD_ref_missed
+    // ratios.  This is detrimental on Illumina, but beneficial on PacBio CCS.
+    // It's possibly related to the homopolyer error likelihoods or overall
+    // Indel accuracy.  Maybe tie this in to the -h option?
+
     r->ori_depth = ori_depth;
     // glfgen
     errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype
+
+    // TODO: account for the number of unassigned reads.  If depth is 50,
+    // but AD is 5,7 then it may look like a variant but it's probably
+    // should be low quality.
+
     return n;
 }
 

bam2bcf.h

@@ -156,7 +156,7 @@ extern "C" {
     int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
     int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
                      const bcf_callaux_t *bca, const char *ref);
-    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
+    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, int ref_len);
     void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call);
 
 #ifdef __cplusplus