Merge remote branch 'main/master'

Conflicts:
	misc/Makefile
	misc/bamcheck.c

diff --combined misc/Makefile
index 64aa9df7c1b6e86fafa14ba7b3040b163175b16f,8a50ea30c9d4f6cfde4a77c0ce3efc00488e269e..e1a5add06a0fb6bc475ec6658d7c8d94e468411e
--- 1/misc/Makefile
--- 2/misc/Makefile
+++ b/misc/Makefile
@@@ -4,7 -4,7 +4,7 @@@ CFLAGS=          -g -Wall -O2 #-m64 #-arch pp
  CXXFLAGS=     $(CFLAGS)
  DFLAGS=               -D_FILE_OFFSET_BITS=64
  OBJS=         
- PROG=         md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim seqtk bamcheck
+ PROG=         md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
  INCLUDES=     -I..
  SUBDIRS=      .
  
@@@ -28,7 -28,7 +28,7 @@@ lib-recur all-recur clean-recur cleanlo
  lib:
  
  bamcheck:bamcheck.o
--              $(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam
++              $(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam -lpthread
  
  bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
                $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
@@@ -36,9 -36,6 +36,6 @@@
  ace2sam:ace2sam.o
                $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
  
- seqtk:seqtk.o
-               $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz
- 
  wgsim:wgsim.o
                $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
  
@@@ -60,9 -57,6 +57,6 @@@ maq2sam-long:maq2sam.
  md5fa.o:md5.h md5fa.c
                $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
  
- seqtk.o:seqtk.c ../khash.h ../kseq.h
-               $(CC) $(CFLAGS) -c -I.. -o $@ seqtk.c
- 
  wgsim.o:wgsim.c ../kseq.h
                $(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c