X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fbamcheck.c;h=76a9f6ee04a8247ebbfd93b35a2e1b0c3e1ca8eb;hb=0ab78ddb98818366103c11330526b8a2ea33a757;hp=03cf3b233fec3b7d976dc07ac82fad94fd47a70c;hpb=7e7b21944f4d89442896d1618f65c22b509c0326;p=samtools.git

diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index 03cf3b2..76a9f6e 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -819,23 +819,23 @@ void output_stats(stats_t *stats)
         printf(" %s",stats->argv[i]);
     printf("\n");
     printf("# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
-    printf("SN\tsequences:\t%ld\n", stats->nreads_1st+stats->nreads_2nd);
+    printf("SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd));
     printf("SN\tis paired:\t%d\n", stats->nreads_1st&&stats->nreads_2nd ? 1 : 0);
     printf("SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
-    printf("SN\t1st fragments:\t%ld\n", stats->nreads_1st);
-    printf("SN\tlast fragments:\t%ld\n", stats->nreads_2nd);
-    printf("SN\treads mapped:\t%ld\n", stats->nreads_paired+stats->nreads_unpaired);
-    printf("SN\treads unmapped:\t%ld\n", stats->nreads_unmapped);
-    printf("SN\treads unpaired:\t%ld\n", stats->nreads_unpaired);
-    printf("SN\treads paired:\t%ld\n", stats->nreads_paired);
-    printf("SN\treads duplicated:\t%ld\n", stats->nreads_dup);
-    printf("SN\treads MQ0:\t%ld\n", stats->nreads_mq0);
-    printf("SN\ttotal length:\t%ld\n", stats->total_len);
-    printf("SN\tbases mapped:\t%ld\n", stats->nbases_mapped);
-    printf("SN\tbases mapped (cigar):\t%ld\n", stats->nbases_mapped_cigar);
-    printf("SN\tbases trimmed:\t%ld\n", stats->nbases_trimmed);
-    printf("SN\tbases duplicated:\t%ld\n", stats->total_len_dup);
-    printf("SN\tmismatches:\t%ld\n", stats->nmismatches);
+    printf("SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st);
+    printf("SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd);
+    printf("SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired+stats->nreads_unpaired));
+    printf("SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped);
+    printf("SN\treads unpaired:\t%ld\n", (long)stats->nreads_unpaired);
+    printf("SN\treads paired:\t%ld\n", (long)stats->nreads_paired);
+    printf("SN\treads duplicated:\t%ld\n", (long)stats->nreads_dup);
+    printf("SN\treads MQ0:\t%ld\n", (long)stats->nreads_mq0);
+    printf("SN\ttotal length:\t%ld\n", (long)stats->total_len);
+    printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped);
+    printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar);
+    printf("SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed);
+    printf("SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup);
+    printf("SN\tmismatches:\t%ld\n", (long)stats->nmismatches);
     printf("SN\terror rate:\t%e\n", (float)stats->nmismatches/stats->nbases_mapped_cigar);
     float avg_read_length = (stats->nreads_1st+stats->nreads_2nd)?stats->total_len/(stats->nreads_1st+stats->nreads_2nd):0;
     printf("SN\taverage length:\t%.0f\n", avg_read_length);
@@ -843,9 +843,9 @@ void output_stats(stats_t *stats)
     printf("SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0);
     printf("SN\tinsert size average:\t%.1f\n", avg_isize);
     printf("SN\tinsert size standard deviation:\t%.1f\n", sd_isize);
-    printf("SN\tinward oriented pairs:\t%ld\n", nisize_inward);
-    printf("SN\toutward oriented pairs:\t%ld\n", nisize_outward);
-    printf("SN\tpairs with other orientation:\t%ld\n", nisize_other);
+    printf("SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
+    printf("SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
+    printf("SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
 
     int ibase,iqual;
     if ( stats->max_len<stats->nbases ) stats->max_len++;
@@ -857,7 +857,7 @@ void output_stats(stats_t *stats)
         printf("FFQ\t%d",ibase+1);
         for (iqual=0; iqual<=stats->max_qual; iqual++)
         {
-            printf("\t%ld", stats->quals_1st[ibase*stats->nquals+iqual]);
+            printf("\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]);
         }
         printf("\n");
     }
@@ -868,7 +868,7 @@ void output_stats(stats_t *stats)
         printf("LFQ\t%d",ibase+1);
         for (iqual=0; iqual<=stats->max_qual; iqual++)
         {
-            printf("\t%ld", stats->quals_2nd[ibase*stats->nquals+iqual]);
+            printf("\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]);
         }
         printf("\n");
     }
@@ -882,7 +882,7 @@ void output_stats(stats_t *stats)
             printf("MPC\t%d",ibase+1);
             for (iqual=0; iqual<=stats->max_qual; iqual++)
             {
-                printf("\t%ld", stats->mpc_buf[ibase*stats->nquals+iqual]);
+                printf("\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]);
             }
             printf("\n");
         }
@@ -892,7 +892,7 @@ void output_stats(stats_t *stats)
     for (ibase=0; ibase<stats->ngc; ibase++)
     {
         if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue;
-        printf("GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1),stats->gc_1st[ibase_prev]);
+        printf("GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]);
         ibase_prev = ibase;
     }
     printf("# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n");
@@ -900,7 +900,7 @@ void output_stats(stats_t *stats)
     for (ibase=0; ibase<stats->ngc; ibase++)
     {
         if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue;
-        printf("GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1),stats->gc_2nd[ibase_prev]);
+        printf("GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]);
         ibase_prev = ibase;
     }
     printf("# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%%]\n");
@@ -913,37 +913,37 @@ void output_stats(stats_t *stats)
     }
     printf("# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
     for (isize=1; isize<ibulk; isize++)
-        printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize,(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
-            stats->isize_inward[isize],stats->isize_outward[isize],stats->isize_other[isize]);
+        printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, (long)(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
+            (long)stats->isize_inward[isize], (long)stats->isize_outward[isize], (long)stats->isize_other[isize]);
 
     printf("# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n");
     int ilen;
     for (ilen=0; ilen<stats->max_len; ilen++)
     {
         if ( stats->read_lengths[ilen]>0 )
-            printf("RL\t%d\t%ld\n", ilen,stats->read_lengths[ilen]);
+            printf("RL\t%d\t%ld\n", ilen, (long)stats->read_lengths[ilen]);
     }
 
     printf("# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n");
     for (ilen=0; ilen<stats->nindels; ilen++)
     {
         if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 )
-            printf("ID\t%d\t%ld\t%ld\n", ilen+1,stats->insertions[ilen],stats->deletions[ilen]);
+            printf("ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]);
     }
 
     printf("# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions, number of deletions\n");
     for (ilen=0; ilen<stats->nbases; ilen++)
     {
         if ( stats->ins_cycles[ilen]>0 || stats->del_cycles[ilen]>0 )
-            printf("IC\t%d\t%ld\t%ld\n", ilen+1,stats->ins_cycles[ilen],stats->del_cycles[ilen]);
+            printf("IC\t%d\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles[ilen], (long)stats->del_cycles[ilen]);
     }
 
     printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
-    printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1,stats->cov[0]);
+    printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
     int icov;
     for (icov=1; icov<stats->ncov-1; icov++)
-        printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1,stats->cov[icov]);
-    printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov[stats->ncov-1]);
+        printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
+    printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
 
 
     // Calculate average GC content, then sort by GC and depth