updated htslib, test, misc.

Makefile

@@ -54,6 +54,7 @@ SOURCES = align\
 		motif_map\
 		multi_partition\
 		needle\
+		normalize\
 		ordered_bcf_overlap_matcher\
 		ordered_region_overlap_matcher\
 		partition\
@@ -96,7 +97,6 @@ SOURCES = align\
    	    tbx_ordered_reader\
     	ahmm\
         xcmp\
-        normalize\
 
 SOURCESONLY = main.cpp
 

annotate_indels.cpp

@@ -185,10 +185,6 @@ class Igor : Program
         std::clog << "         [m] mode                  " << mode << "\n";
         print_boo_op("         [d] debug                 ", debug);
         print_ref_op("         [r] ref FASTA file        ", ref_fasta_file);
-
-        std::clog << "         [m] mode    dfsdasdad     " << mode << "\n";
-
-
         print_boo_op("         [x] override tag          ", override_tag);        
         print_boo_op("         [v] add vntr record       ", add_vntr_record);        
 
@@ -205,18 +201,19 @@ class Igor : Program
 
     void insert_vntr_record(bcf_hdr_t* h, bcf1_t *v, Variant& variant)
     {
-//        bcf_update_info_string(h, v, MOTIF.c_str(), vntr.motif.c_str());
-//        bcf_update_info_string(h, v, RU.c_str(), vntr.ru.c_str());
-//        bcf_update_info_float(h, v, RL.c_str(), &vntr.rl, 1);
-//        bcf_update_info_string(h, v, REF.c_str(), vntr.repeat_tract.seq.c_str());
-//        bcf_update_info_int32(h, v, REFPOS.c_str(), &vntr.repeat_tract.pos1, 1);
-//        kstring_t new_alleles = {0,0,0};
-//        kputs(vntr.repeat_tract.seq.c_str(), &new_alleles);
-//        kputc(',', &new_alleles);
-//        kputs("<VNTR>", &new_alleles);
-//        bcf_update_alleles_str(h, v, new_alleles.s);
-//        bcf_set_pos1(v, vntr.repeat_tract.pos1);
-//        if (new_alleles.m) free(new_alleles.s);
+        VNTR& vntr = variant.vntr;
+        bcf_update_info_string(h, v, MOTIF.c_str(), vntr.motif.c_str());
+        bcf_update_info_string(h, v, RU.c_str(), vntr.ru.c_str());
+        bcf_update_info_float(h, v, RL.c_str(), &vntr.rl, 1);
+        bcf_update_info_string(h, v, REF.c_str(), vntr.repeat_tract.seq.c_str());
+        bcf_update_info_int32(h, v, REFPOS.c_str(), &vntr.repeat_tract.pos1, 1);
+        kstring_t new_alleles = {0,0,0};
+        kputs(vntr.repeat_tract.seq.c_str(), &new_alleles);
+        kputc(',', &new_alleles);
+        kputs("<VNTR>", &new_alleles);
+        bcf_update_alleles_str(h, v, new_alleles.s);
+        bcf_set_pos1(v, vntr.repeat_tract.pos1);
+        if (new_alleles.m) free(new_alleles.s);
     }
 
     void annotate_indels()
@@ -240,6 +237,7 @@ class Igor : Program
 
                 if (add_vntr_record)
                 {
+
                     insert_vntr_record(odr->hdr, v, variant);
                     odw->write(v);
                     v = odw->get_bcf1_from_pool();

lib/htslib/cram/cram_decode.c

@@ -726,7 +726,7 @@ int cram_dependent_data_series(cram_fd *fd,
 	    fd->decode_md = 0;
 
 	if (fd->required_fields & SAM_QUAL)
-	    hdr->data_series |= CRAM_SEQ;
+	    hdr->data_series |= CRAM_QUAL;
 
 	if (fd->required_fields & SAM_AUX)
 	    hdr->data_series |= CRAM_RG | CRAM_TL | CRAM_aux;

lib/htslib/cram/cram_io.c

@@ -3014,6 +3014,9 @@ int cram_write_container(cram_fd *fd, cram_container *c) {
 static int cram_flush_container2(cram_fd *fd, cram_container *c) {
     int i, j;
 
+    if (c->curr_slice > 0 && !c->slices)
+	return -1;
+
     //fprintf(stderr, "Writing container %d, sum %u\n", c->record_counter, sum);
 
     /* Write the container struct itself */
@@ -4255,7 +4258,7 @@ int cram_eof(cram_fd *fd) {
  * Returns 0 on success
  *        -1 on failure
  */
-int cram_set_option(cram_fd *fd, enum cram_option opt, ...) {
+int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...) {
     int r;
     va_list args;
 
@@ -4273,7 +4276,7 @@ int cram_set_option(cram_fd *fd, enum cram_option opt, ...) {
  * Returns 0 on success
  *        -1 on failure
  */
-int cram_set_voption(cram_fd *fd, enum cram_option opt, va_list args) {
+int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
     refs_t *refs;
 
     if (!fd)
@@ -4406,6 +4409,10 @@ int cram_set_voption(cram_fd *fd, enum cram_option opt, va_list args) {
 	fd->required_fields = va_arg(args, int);
 	break;
 
+    case HTS_OPT_COMPRESSION_LEVEL:
+	fd->level = va_arg(args, int);
+	break;
+
     default:
 	fprintf(stderr, "Unknown CRAM option code %d\n", opt);
 	return -1;

lib/htslib/cram/cram_io.h

@@ -609,7 +609,7 @@ int cram_eof(cram_fd *fd);
  * Returns 0 on success;
  *        -1 on failure
  */
-int cram_set_option(cram_fd *fd, enum cram_option opt, ...);
+int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...);
 
 /*! Sets options on the cram_fd.
  *
@@ -620,7 +620,7 @@ int cram_set_option(cram_fd *fd, enum cram_option opt, ...);
  * Returns 0 on success;
  *        -1 on failure
  */
-int cram_set_voption(cram_fd *fd, enum cram_option opt, va_list args);
+int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args);
 
 /*!
  * Attaches a header to a cram_fd.

lib/htslib/cram/cram_structs.h

@@ -771,8 +771,10 @@ enum cram_fields {
 #define CRAM_CIGAR (CRAM_FN | CRAM_FP | CRAM_FC | CRAM_DL | CRAM_IN | \
 		    CRAM_SC | CRAM_HC | CRAM_PD | CRAM_RS | CRAM_RL | CRAM_BF)
 
-#define CRAM_SEQ (CRAM_CIGAR | CRAM_BA | CRAM_QS | CRAM_BS | \
-		  CRAM_RL    | CRAM_AP | CRAM_BB | CRAM_QQ)
+#define CRAM_SEQ (CRAM_CIGAR | CRAM_BA | CRAM_BS | \
+		  CRAM_RL    | CRAM_AP | CRAM_BB)
+
+#define CRAM_QUAL (CRAM_CIGAR | CRAM_RL | CRAM_AP | CRAM_QS | CRAM_QQ)
 
 /* BF bitfields */
 /* Corrected in 1.1. Use bam_flag_swap[bf] and BAM_* macros for 1.0 & 1.1 */