Update for bl_sam_init() API change

auerlab · Apr 5, 2022 · 16ae5d5 · 16ae5d5
1 parent 795f607
commit 16ae5d5
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/Makefile b/Makefile
@@ -92,7 +92,7 @@ CPP         ?= cpp
 AR          ?= ar
 RANLIB      ?= ranlib
 
-INCLUDES    += -isystem ${LOCALBASE}/include -I/usr/local/include
+INCLUDES    += -isystem ${PREFIX}/include -isystem ${LOCALBASE}/include
 CFLAGS      += ${INCLUDES}
 CXXFLAGS    += ${INCLUDES}
 FFLAGS      += ${INCLUDES}

diff --git a/ad2vcf.c b/ad2vcf.c
@@ -243,7 +243,7 @@ int     ad2vcf(const char *argv[], FILE *sam_stream)
 #ifdef DEBUG
     static bl_sam_t sam_alignment = BL_SAM_ALIGNMENT_INIT;
     if ( sam_alignment.seq == NULL )
-	bl_sam_init(&sam_alignment, BL_SAM_SEQ_MAX_CHARS, REQUIRED_SAM_FIELDS);
+	bl_sam_init(&sam_alignment);
 
     // Debug discarded count
     puts("Gathering stats on trailing alignments...");
@@ -332,10 +332,10 @@ int     skip_upstream_alignments(bl_vcf_t *vcf_call, FILE *sam_stream,
     size_t          c;
     bool            ma = true;
     // static so sam_alignment_read() won't keep reallocating seq
-    static bl_sam_t sam_alignment = BL_SAM_ALIGNMENT_INIT;
+    static bl_sam_t sam_alignment = BL_SAM_INIT;
 
     if ( sam_alignment.seq == NULL )
-	bl_sam_init(&sam_alignment, BL_SAM_SEQ_MAX_CHARS, REQUIRED_SAM_FIELDS);
+	bl_sam_init(&sam_alignment);
 
     /*
      *  Check and discard already buffered alignments upstream of the given
@@ -424,10 +424,10 @@ int     allelic_depth(bl_vcf_t *vcf_call, FILE *sam_stream,
     size_t          c;
     bool            ma = true, overlapping = true;
     // static so sam_alignment_read() won't keep reallocating seq
-    static bl_sam_t sam_alignment = BL_SAM_ALIGNMENT_INIT;
+    static bl_sam_t sam_alignment = BL_SAM_INIT;
 
     if ( sam_alignment.seq == NULL )
-	bl_sam_init(&sam_alignment, BL_SAM_SEQ_MAX_CHARS, REQUIRED_SAM_FIELDS);
+	bl_sam_init(&sam_alignment);
 
     /* Check and discard already buffered alignments */
     for (c = 0; (c < BL_SAM_BUFF_BUFFERED_COUNT(sam_buff)) &&