From: Heng Li <lh3@live.co.uk>
Date: Tue, 17 Aug 2010 00:53:16 +0000 (+0000)
Subject: use float for QUAL
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=af4483bd3b8b7da708baf521a75b6531a0a8bd0a;p=samtools.git

use float for QUAL
---

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index c331388..e375a1f 100644
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -146,13 +146,12 @@ int bcf_sync(int n_smpl, bcf1_t *b)
 
 int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 {
-	uint32_t x;
 	int i, l = 0;
 	if (b == 0) return -1;
 	bgzf_write(bp->fp, &b->tid, 4);
 	bgzf_write(bp->fp, &b->pos, 4);
-	x = b->qual<<24 | b->l_str;
-	bgzf_write(bp->fp, &x, 4);
+	bgzf_write(bp->fp, &b->qual, 4);
+	bgzf_write(bp->fp, &b->l_str, 4);
 	bgzf_write(bp->fp, b->str, b->l_str);
 	l = 12 + b->l_str;
 	for (i = 0; i < b->n_gi; ++i) {
@@ -165,12 +164,11 @@ int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 {
 	int i, l = 0;
-	uint32_t x;
 	if (b == 0) return -1;
 	if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
 	bgzf_read(bp->fp, &b->pos, 4);
-	bgzf_read(bp->fp, &x, 4);
-	b->qual = x >> 24; b->l_str = x << 8 >> 8;
+	bgzf_read(bp->fp, &b->qual, 4);
+	bgzf_read(bp->fp, &b->l_str, 4);
 	if (b->l_str > b->m_str) {
 		b->m_str = b->l_str;
 		kroundup32(b->m_str);
diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index c317440..8e4ecf9 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -14,8 +14,8 @@ typedef struct {
 
 typedef struct {
 	int32_t tid, pos;
-	uint32_t qual:8, l_str:24;
-	int m_str;
+	int32_t l_str, m_str;
+	float qual;
 	char *str, *ref, *alt, *flt, *info, *fmt; // fmt, ref, alt and info point to str
 	int n_gi, m_gi;
 	bcf_ginfo_t *gi;
diff --git a/bcftools/bcf.tex b/bcftools/bcf.tex
index b4bec72..5ca1e28 100644
--- a/bcftools/bcf.tex
+++ b/bcftools/bcf.tex
@@ -24,7 +24,8 @@
 \multicolumn{5}{|c|}{\it \color{gray}{List of records until the end of the file}}\\\cline{2-5}
 & {\tt seq\_id} & Reference sequence ID & {\tt int32\_t} & \\\cline{2-5}
 & {\tt pos} & Position & {\tt int32\_t} & \\\cline{2-5}
-& {\tt qual\_slen} & {\tt varQual\char60\char60 24 | slen} & {\tt uint32\_t} & \\\cline{2-5}
+& {\tt qual} & Variant quality & {\tt float} & \\\cline{2-5}
+& {\tt l\_str} & Length of str & {\tt int32\_t} & \\\cline{2-5}
 & {\tt str} & {\tt ID+REF+ALT+FILTER+INFO+FORMAT}, {\tt NULL} padded & {\tt char[slen]} &\\\cline{2-5}
 & \multicolumn{4}{c|}{Blocks of data; \#blocks and formats defined by {\tt FORMAT} (table below)}\\
 \hline