From 9b352ed762c83f3df15cb385e0355930f6362074 Mon Sep 17 00:00:00 2001 From: peterjc Date: Tue, 19 Jun 2012 12:42:50 +0100 Subject: [PATCH] Update @SQ lines during 'samtools depad' Note does not (yet) preserve additional @SQ line tags (e.g. AS, SP, UR). --- padding.c | 42 ++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 40 insertions(+), 2 deletions(-) diff --git a/padding.c b/padding.c index 23d1b23..b7a254f 100644 --- a/padding.c +++ b/padding.c @@ -295,10 +295,48 @@ bam_header_t * fix_header(bam_header_t *old, faidx_t *fai) fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]); } else { header->target_len[i] = unpadded_len; - fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]); + //fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]); } } - /* TODO - Correct the @SQ reference lengths from padded to unpadded */ + /* Duplicating the header allocated new buffer for header string */ + /* After modifying the @SQ lines it will only get smaller, since */ + /* the LN entries will be the same or shorter, and we'll remove */ + /* any MD entries (MD5 checksums). */ + assert(strlen(old->text) == strlen(header->text)); + assert (0==strcmp(old->text, header->text)); + const char *text; + text = old->text; + header->text[0] = '\0'; /* Resuse the allocated buffer */ + char * newtext = header->text; + char * end=NULL; + while (text[0]=='@') { + end = strchr(text, '\n'); + assert(end != 0); + if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') { + /* TODO - edit the @SQ line here to remove MD and fix LN. */ + /* For now just remove the @SQ line, and samtools will */ + /* automatically generate a minimal replacement with LN. */ + /* However, that discards any other tags like AS, SP, UR. */ + //fprintf(stderr, "[depad] Removing @SQ line\n"); + } else { + /* Copy this line to the new header */ + strncat(newtext, text, end - text + 1); + } + text = end + 1; + } + assert (text[0]=='\0'); + /* Check we didn't overflow the buffer */ + assert (strlen(header->text) <= strlen(old->text)); + if (strlen(header->text) < header->l_text) { + //fprintf(stderr, "[depad] Reallocating header buffer\n"); + assert (newtext == header->text); + newtext = calloc(strlen(header->text) + 1, 1); + strcpy(newtext, header->text); + free(header->text); + header->text = newtext; + header->l_text = strlen(newtext); + } + //fprintf(stderr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text); return header; } -- 2.39.2