1 files changed, 38 insertions, 37 deletions

diff --git a/biology/iolib/pkg-plist b/biology/iolib/pkg-plist
index 66c175cb6c28..aa9a99fba0bf 100644
--- a/biology/iolib/pkg-plist
+++ b/biology/iolib/pkg-plist
@@ -1,8 +1,43 @@
+bin/append_sff
+bin/convert_trace
+bin/cram_dump
+bin/cram_index
+bin/extract_fastq
+bin/extract_qual
+bin/extract_seq
+bin/get_comment
+bin/hash_exp
+bin/hash_extract
+bin/hash_list
+bin/hash_sff
+bin/hash_tar
+bin/index_tar
+bin/io_lib-config
+bin/makeSCF
+bin/scf_dump
+bin/scf_info
+bin/scf_update
+bin/scram_flagstat
+bin/scram_merge
+bin/scram_pileup
+bin/scramble
+bin/srf2fasta
+bin/srf2fastq
+bin/srf_dump_all
+bin/srf_extract_hash
+bin/srf_extract_linear
+bin/srf_filter
+bin/srf_index_hash
+bin/srf_info
+bin/srf_list
+bin/trace_dump
+bin/ztr_dump
 include/io_lib/Read.h
 include/io_lib/abi.h
 include/io_lib/alf.h
 include/io_lib/array.h
 include/io_lib/bam.h
+include/io_lib/binning.h
 include/io_lib/compress.h
 include/io_lib/compression.h
 include/io_lib/cram.h
@@ -11,6 +46,7 @@ include/io_lib/cram_decode.h
 include/io_lib/cram_encode.h
 include/io_lib/cram_index.h
 include/io_lib/cram_io.h
+include/io_lib/cram_stats.h
 include/io_lib/cram_structs.h
 include/io_lib/deflate_interlaced.h
 include/io_lib/dstring.h
@@ -33,57 +69,22 @@ include/io_lib/scf.h
 include/io_lib/scf_extras.h
 include/io_lib/scram.h
 include/io_lib/seqIOABI.h
-include/io_lib/seqIOCTF.h
 include/io_lib/sff.h
 include/io_lib/srf.h
 include/io_lib/stdio_hack.h
 include/io_lib/string_alloc.h
 include/io_lib/tar_format.h
+include/io_lib/thread_pool.h
 include/io_lib/traceType.h
 include/io_lib/translate.h
 include/io_lib/vlen.h
 include/io_lib/xalloc.h
 include/io_lib/zfio.h
 include/io_lib/ztr.h
-bin/append_sff
-bin/convert_trace
-bin/cram_dump
-bin/cram_index
-bin/cram_to_sam
-bin/extract_fastq
-bin/extract_qual
-bin/extract_seq
-bin/get_comment
-bin/hash_exp
-bin/hash_extract
-bin/hash_list
-bin/hash_sff
-bin/hash_tar
-bin/index_tar
-bin/io_lib-config
-bin/makeSCF
-bin/sam_convert
-bin/sam_to_cram
-bin/scf_dump
-bin/scf_info
-bin/scf_update
-bin/scram_merge
-bin/scramble
-bin/srf2fasta
-bin/srf2fastq
-bin/srf_dump_all
-bin/srf_extract_hash
-bin/srf_extract_linear
-bin/srf_filter
-bin/srf_index_hash
-bin/srf_info
-bin/srf_list
-bin/trace_dump
-bin/ztr_dump
 lib/libstaden-read.a
 lib/libstaden-read.la
 lib/libstaden-read.so
-lib/libstaden-read.so.3
+lib/libstaden-read.so.5
 man/man1/scramble.1.gz
 man/man1/srf2fasta.1.gz
 man/man1/srf2fastq.1.gz