- Fixed biod#328

- Updated to BioD latest and added RELEASE NOTES
pjotrp · Feb 7, 2018 · 1447403 · 1447403
1 parent bebb8f6
commit 1447403
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/BioD b/BioD
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -7,4 +7,9 @@ large files. See also [performance](https://github.com/biod/sambamba/blob/master
 + Fixed Makefile for general use, see #332
 + Started benchmarking, see #283 and https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org
 + Readded [Travis-ci support](https://travis-ci.org/biod/sambamba) for Linux (MacOS is disabled #338)
++ Updated BioD to latest https://github.com/biod/BioD/commit/5e56b2bb45324af2194b3339d298fd827c8003ae
++ Bug fixes:
+  * #328 Debug version: SAM output of CRAM file is populated with debug on pipe
+  * #331 Segmentation fault attempting to view header in json format
+  * #335 Intel Xeon bug may segfault Sambamba - this was tracked down to an Intel Xeon bug
 + Documentation updates
diff --git a/cram/wrappers.d b/cram/wrappers.d
@@ -51,7 +51,7 @@ struct RcPtr(T, alias Free) {
     this(this)
     {
         static if (is(T == cram_slice)) {
-            debug writeln("COPIED #", data.payload_id + 1);
+            debug stderr.writeln("COPIED #", data.payload_id + 1);
         }
     }
 
@@ -159,7 +159,7 @@ struct CramContainerRange {
         auto err_msg = "Failed to read container header";
         while (true) {
             // read container header
-            debug writeln("cram_read_container");
+            debug stderr.writeln("cram_read_container");
             auto ptr = nullChecked!cram_read_container(err_msg, _fd);
             if (ptr is null) {
                 empty = true;
+19 −11		README.md
+1 −0		bio/bam/baseinfo.d
+290 −0		bio/bam/cigar.d
+29 −28		bio/bam/md/reconstruct.d
+2 −1		bio/bam/pileup.d
+3 −229		bio/bam/read.d
+1 −1		bio/bam/utils/samheadermerger.d
+1 −1		bio/core/bgzf/compress.d
+151 −0		bio/core/fastq.d
+159 −129		bio/core/region.d
+72 −0		bio/core/utils/exception.d
+1 −1		bio/core/utils/format.d
+5 −3		bio/core/utils/roundbuf.d
+52 −49		bio/sam/header.d
+233 −232		bio/sam/utils/fastrecordparser.d
+32 −31		bio/sam/utils/recordparser.d
+6 −1		examples/calculate_gc_content_from_reference.d
+7 −1		examples/create_bam_from_scratch.d
+6 −1		examples/iterate_tags.d
+6 −1		examples/make_pileup.d
+6 −1		examples/print_base_info.d
+6 −1		examples/read_bam_file.d
+6 −1		examples/transverse_multiple_bam_files.d
+5 −2		src_ragel/Makefile
+28 −27		src_ragel/sam_alignment.rl
+24 −23		test/unittests.d