combine微型计算机pp200,combine-diff.c

#include "cache.h"

#include "object-store.h"

#include "commit.h"

#include "blob.h"

#include "diff.h"

#include "diffcore.h"

#include "quote.h"

#include "xdiff-interface.h"

#include "xdiff/xmacros.h"

#include "log-tree.h"

#include "refs.h"

#include "userdiff.h"

#include "sha1-array.h"

#include "revision.h"

static int compare_paths(const struct combine_diff_path *one,

const struct diff_filespec *two)

{

if (!S_ISDIR(one->mode) && !S_ISDIR(two->mode))

return strcmp(one->path, two->path);

return base_name_compare(one->path, strlen(one->path), one->mode,

two->path, strlen(two->path), two->mode);

}

static int filename_changed(char status)

{

return status == 'R' || status == 'C';

}

static struct combine_diff_path *intersect_paths(

struct combine_diff_path *curr,

int n,

int num_parent,

int combined_all_paths)

{

struct diff_queue_struct *q = &diff_queued_diff;

struct combine_diff_path *p, **tail = &curr;

int i, j, cmp;

if (!n) {

for (i = 0; i < q->nr; i++) {

int len;

const char *path;

if (diff_unmodified_pair(q->queue[i]))

continue;

path = q->queue[i]->two->path;

len = strlen(path);

p = xmalloc(combine_diff_path_size(num_parent, len));

p->path = (char *) &(p->parent[num_parent]);

memcpy(p->path, path, len);

p->path[len] = 0;

p->next = NULL;

memset(p->parent, 0,

sizeof(p->parent[0]) * num_parent);

oidcpy(&p->oid, &q->queue[i]->two->oid);

p->mode = q->queue[i]->two->mode;

oidcpy(&p->parent[n].oid, &q->queue[i]->one->oid);

p->parent[n].mode = q->queue[i]->one->mode;

p->parent[n].status = q->queue[i]->status;

if (combined_all_paths &&

filename_changed(p->parent[n].status)) {

strbuf_init(&p->parent[n].path, 0);

strbuf_addstr(&p->parent[n].path,

q->queue[i]->one->path);

}

*tail = p;

tail = &p->next;

}

return curr;

}

/*

* paths in curr (linked list) and q->queue[] (array) are

* both sorted in the tree order.

*/

i = 0;

while ((p = *tail) != NULL) {

cmp = ((i >= q->nr)

? -1 : compare_paths(p, q->queue[i]->two));

if (cmp < 0) {

/* p->path not in q->queue[]; drop it */

*tail = p->next;

for (j = 0; j < num_parent; j++)

if (combined_all_paths &&

filename_changed(p->parent[j].status))

strbuf_release(&p->parent[j].path);

free(p);

continue;

}

if (cmp > 0) {

/* q->queue[i] not in p->path; skip it */

i++;

continue;

}

oidcpy(&p->parent[n].oid, &q->queue[i]->one->oid);

p->parent[n].mode = q->queue[i]->one->mode;

p->parent[n].status = q->queue[i]->status;

if (combined_all_paths &&

filename_changed(p->parent[n].status))

strbuf_addstr(&p->parent[n].path,

q->queue[i]->one->path);

tail = &p->next;

i++;

}

return curr;

}

/* Lines lost from parent */

struct lline {

struct lline *next, *prev;

int len;

unsigned long parent_map;

char line[FLEX_ARRAY];

};

/* Lines lost from current parent (before coalescing) */

struct plost {

struct lline *lost_head, *lost_tail;

int len;

};

/* Lines surviving in the merge result */

struct sline {

/* Accumulated and coalesced lost lines */

struct lline *lost;

int lenlost;

struct plost plost;

char *bol;

int len;

/* bit 0 up to (N-1) are on if the parent has this line (i.e.

* we did not change it).

* bit N is used for "interesting" lines, including context.

* bit (N+1) is used for "do not show deletion before this".

*/

unsigned long flag;

unsigned long *p_lno;

};

static int match_string_spaces(const char *line1, int len1,

const char *line2, int len2,

long flags)

{

if (flags & XDF_WHITESPACE_FLAGS) {

for (; len1 > 0 && XDL_ISSPACE(line1[len1 - 1]); len1--);

for (; len2 > 0 && XDL_ISSPACE(line2[len2 - 1]); len2--);

}

if (!(flags & (XDF_IGNORE_WHITESPACE | XDF_IGNORE_WHITESPACE_CHANGE)))

return (len1 == len2 && !memcmp(line1, line2, len1));

while (len1 > 0 && len2 > 0) {

len1--;

len2--;

if (XDL_ISSPACE(line1[len1]) || XDL_ISSPACE(line2[len2])) {

if ((flags & XDF_IGNORE_WHITESPACE_CHANGE) &&

(!XDL_ISSPACE(line1[len1]) || !XDL_ISSPACE(line2[len2])))

return 0;

for (; len1 > 0 && XDL_ISSPACE(line1[len1]); len1--);

for (; len2 > 0 && XDL_ISSPACE(line2[len2]); len2--);

}

if (line1[len1] != line2[len2])

return 0;

}

if (flags & XDF_IGNORE_WHITESPACE) {

/* Consume remaining spaces */

for (; len1 > 0 && XDL_ISSPACE(line1[len1 - 1]); len1--);

for (; len2 > 0 && XDL_ISSPACE(line2[len2 - 1]); len2--);

}

/* We matched full line1 and line2 */

if (!len1 && !len2)

return 1;

return 0;

}

enum coalesce_direction { MATCH, BASE, NEW };

/* Coalesce new lines into base by finding LCS */

static struct lline *coalesce_lines(struct lline *base, int *lenbase,

struct lline *newline, int lennew,

unsigned long parent, long flags)

{

int **lcs;

enum coalesce_direction **directions;

struct lline *baseend, *newend = NULL;

int i, j, origbaselen = *lenbase;

if (newline == NULL)

return base;

if (base == NULL) {

*lenbase = lennew;

return newline;

}

/*

* Coalesce new lines into base by finding the LCS

* - Create the table to run dynamic programming

* - Compute the LCS

* - Then reverse read the direction structure:

* - If we have MATCH, assign parent to base flag, and consume

* both baseend and newend

* - Else if we have BASE, consume baseend

* - Else if we have NEW, insert newend lline into base and

* consume newend

*/

lcs = xcalloc(st_add(origbaselen, 1), sizeof(int*));

directions = xcalloc(st_add(origbaselen, 1), sizeof(enum coalesce_direction*));

for (i = 0; i < origbaselen + 1; i++) {

lcs[i] = xcalloc(st_add(lennew, 1), sizeof(int));

directions[i] = xcalloc(st_add(lennew, 1), sizeof(enum coalesce_direction));

directions[i][0] = BASE;

}

for (j = 1; j < lennew + 1; j++)

directions[0][j] = NEW;

for (i = 1, baseend = base; i < origbaselen + 1; i++) {

for (j = 1, newend = newline; j < lennew + 1; j++) {

if (match_string_spaces(baseend->line, baseend->len,

newend->line, newend->len, flags)) {

lcs[i][j] = lcs[i - 1][j - 1] + 1;

directions[i][j] = MATCH;

} else if (lcs[i][j - 1] >= lcs[i - 1][j]) {

lcs[i][j] = lcs[i][j - 1];

directions[i][j] = NEW;

} else {

lcs[i][j] = lcs[i - 1][j];

directions[i][j] = BASE;

}

if (newend->next)

newend = newend->next;

}

if (baseend->next)

baseend = baseend->next;

}

for (i = 0; i < origbaselen + 1; i++)

free(lcs[i]);

free(lcs);

/* At this point, baseend and newend point to the end of each lists */

i--;

j--;

while (i != 0 || j != 0) {

if (directions[i][j] == MATCH) {

baseend->parent_map |= 1<

baseend = baseend->prev;

newend = newend->prev;

i--;

j--;

} else if (directions[i][j] == NEW) {

struct lline *lline;

lline = newend;

/* Remove lline from new list and update newend */

if (lline->prev)

lline->prev->next = lline->next;

else

newline = lline->next;

if (lline->next)

lline->next->prev = lline->prev;

newend = lline->prev;

j--;

/* Add lline to base list */

if (baseend) {

lline->next = baseend->next;

lline->prev = baseend;

if (lline->prev)

lline->prev->next = lline;

}

else {

lline->next = base;

base = lline;

}

(*lenbase)++;

if (lline->next)

lline->next->prev = lline;

} else {

baseend = baseend->prev;

i--;

}

}

newend = newline;

while (newend) {

struct lline *lline = newend;

newend = newend->next;

free(lline);

}

for (i = 0; i < origbaselen + 1; i++)

free(directions[i]);

free(directions);

return base;

}

static char *grab_blob(struct repository *r,

const struct object_id *oid, unsigned int mode,

unsigned long *size, struct userdiff_driver *textconv,

const char *path)

{

char *blob;

enum object_type type;

if (S_ISGITLINK(mode)) {

struct strbuf buf = STRBUF_INIT;

strbuf_addf(&buf, "Subproject commit %s\n", oid_to_hex(oid));

*size = buf.len;

blob = strbuf_detach(&buf, NULL);

} else if (is_null_oid(oid)) {

/* deleted blob */

*size = 0;

return xcalloc(1, 1);

} else if (textconv) {

struct diff_filespec *df = alloc_filespec(path);

fill_filespec(df, oid, 1, mode);

*size = fill_textconv(r, textconv, df, &blob);

free_filespec(df);

} else {

blob = read_object_file(oid, &type, size);

if (type != OBJ_BLOB)

die("object '%s' is not a blob!", oid_to_hex(oid));

}

return blob;

}

static void append_lost(struct sline *sline, int n, const char *line, int len)

{

struct lline *lline;

unsigned long this_mask = (1UL<

if (line[len-1] == '\n')

len--;

FLEX_ALLOC_MEM(lline, line, line, len);

lline->len = len;

lline->next = NULL;

lline->prev = sline->plost.lost_tail;

if (lline->prev)

lline->prev->next = lline;

else

sline->plost.lost_head = lline;

sline->plost.lost_tail = lline;

sline->plost.len++;

lline->parent_map = this_mask;

}

struct combine_diff_state {

unsigned int lno;

int ob, on, nb, nn;

unsigned long nmask;

int num_parent;

int n;

struct sline *sline;

struct sline *lost_bucket;

};

static void consume_hunk(void *state_,

long ob, long on,

long nb, long nn,

const char *funcline, long funclen)

{

struct combine_diff_state *state = state_;

state->ob = ob;

state->on = on;

state->nb = nb;

state->nn = nn;

state->lno = state->nb;

if (state->nn == 0) {

/* @@ -X,Y +N,0 @@ removed Y lines

* that would have come *after* line N

* in the result. Our lost buckets hang

* to the line after the removed lines,

*

* Note that this is correct even when N == 0,

* in which case the hunk removes the first

* line in the file.

*/

state->lost_bucket = &state->sline[state->nb];

if (!state->nb)

state->nb = 1;

} else {

state->lost_bucket = &state->sline[state->nb-1];

}

if (!state->sline[state->nb-1].p_lno)

state->sline[state->nb-1].p_lno =

xcalloc(state->num_parent, sizeof(unsigned long));

state->sline[state->nb-1].p_lno[state->n] = state->ob;

}

static void consume_line(void *state_, char *line, unsigned long len)

{

struct combine_diff_state *state = state_;

if (!state->lost_bucket)

return; /* not in any hunk yet */

switch (line[0]) {

case '-':

append_lost(state->lost_bucket, state->n, line+1, len-1);

break;

case '+':

state->sline[state->lno-1].flag |= state->nmask;

state->lno++;

break;

}

}

static void combine_diff(struct repository *r,

const struct object_id *parent, unsigned int mode,

mmfile_t *result_file,

struct sline *sline, unsigned int cnt, int n,

int num_parent, int result_deleted,

struct userdiff_driver *textconv,

const char *path, long flags)

{

unsigned int p_lno, lno;

unsigned long nmask = (1UL << n);

xpparam_t xpp;

xdemitconf_t xecfg;

mmfile_t parent_file;

struct combine_diff_state state;

unsigned long sz;

if (result_deleted)

return; /* result deleted */

parent_file.ptr = grab_blob(r, parent, mode, &sz, textconv, path);

parent_file.size = sz;

memset(&xpp, 0, sizeof(xpp));

xpp.flags = flags;

memset(&xecfg, 0, sizeof(xecfg));

memset(&state, 0, sizeof(state));

state.nmask = nmask;

state.sline = sline;

state.lno = 1;

state.num_parent = num_parent;

state.n = n;

if (xdi_diff_outf(&parent_file, result_file, consume_hunk,

consume_line, &state, &xpp, &xecfg))

die("unable to generate combined diff for %s",

oid_to_hex(parent));

free(parent_file.ptr);

/* Assign line numbers for this parent.

*

* sline[lno].p_lno[n] records the first line number

* (counting from 1) for parent N if the final hunk display

* started by showing sline[lno] (possibly showing the lost

* lines attached to it first).

*/

for (lno = 0, p_lno = 1; lno <= cnt; lno++) {

struct lline *ll;

sline[lno].p_lno[n] = p_lno;

/* Coalesce new lines */

if (sline[lno].plost.lost_head) {

struct sline *sl = &sline[lno];

sl->lost = coalesce_lines(sl->lost, &sl->lenlost,

sl->plost.lost_head,

sl->plost.len, n, flags);

sl->plost.lost_head = sl->plost.lost_tail = NULL;

sl->plost.len = 0;

}

/* How many lines would this sline advance the p_lno? */

ll = sline[lno].lost;

while (ll) {

if (ll->parent_map & nmask)

p_lno++; /* '-' means parent had it */

ll = ll->next;

}

if (lno < cnt && !(sline[lno].flag & nmask))

p_lno++; /* no '+' means parent had it */

}

sline[lno].p_lno[n] = p_lno; /* trailer */

}

static unsigned long context = 3;

static char combine_marker = '@';

static int interesting(struct sline *sline, unsigned long all_mask)

{

/* If some parents lost lines here, or if we have added to

* some parent, it is interesting.

*/

return ((sline->flag & all_mask) || sline->lost);

}

static unsigned long adjust_hunk_tail(struct sline *sline,

unsigned long all_mask,

unsigned long hunk_begin,

unsigned long i)

{

/* i points at the first uninteresting line. If the last line

* of the hunk was interesting only because it has some

* deletion, then it is not all that interesting for the

* purpose of giving trailing context lines. This is because

* we output '-' line and then unmodified sline[i-1] itself in

* that case which gives us one extra context line.

*/

if ((hunk_begin + 1 <= i) && !(sline[i-1].flag & all_mask))

i--;

return i;

}

static unsigned long find_next(struct sline *sline,

unsigned long mark,

unsigned long i,

unsigned long cnt,

int look_for_uninteresting)

{

/* We have examined up to i-1 and are about to look at i.

* Find next interesting or uninteresting line. Here,

* "interesting" does not mean interesting(), but marked by

* the give_context() function below (i.e. it includes context

* lines that are not interesting to interesting() function

* that are surrounded by interesting() ones.

*/

while (i <= cnt)

if (look_for_uninteresting

? !(sline[i].flag & mark)

: (sline[i].flag & mark))

return i;

else

i++;

return i;

}

static int give_context(struct sline *sline, unsigned long cnt, int num_parent)

{

unsigned long all_mask = (1UL<

unsigned long mark = (1UL<

unsigned long no_pre_delete = (2UL<

unsigned long i;

/* Two groups of interesting lines may have a short gap of

* uninteresting lines. Connect such groups to give them a

* bit of context.

*

* We first start from what the interesting() function says,

* and mark them with "mark", and paint context lines with the

* mark. So interesting() would still say false for such context

* lines but they are treated as "interesting" in the end.

*/

i = find_next(sline, mark, 0, cnt, 0);

if (cnt < i)

return 0;

while (i <= cnt) {

unsigned long j = (context < i) ? (i - context) : 0;

unsigned long k;

/* Paint a few lines before the first interesting line. */

while (j < i) {

if (!(sline[j].flag & mark))

sline[j].flag |= no_pre_delete;

sline[j++].flag |= mark;

}

again:

/* we know up to i is to be included. where does the

* next uninteresting one start?

*/

j = find_next(sline, mark, i, cnt, 1);

if (cnt < j)

break; /* the rest are all interesting */

/* lookahead context lines */

k = find_next(sline, mark, j, cnt, 0);

j = adjust_hunk_tail(sline, all_mask, i, j);

if (k < j + context) {

/* k is interesting and [j,k) are not, but

* paint them interesting because the gap is small.

*/

while (j < k)

sline[j++].flag |= mark;

i = k;

goto again;

}

/* j is the first uninteresting line and there is

* no overlap beyond it within context lines. Paint

* the trailing edge a bit.

*/

i = k;

k = (j + context < cnt+1) ? j + context : cnt+1;

while (j < k)

sline[j++].flag |= mark;

}

return 1;

}

static int make_hunks(struct sline *sline, unsigned long cnt,

int num_parent, int dense)

{

unsigned long all_mask = (1UL<

unsigned long mark = (1UL<

unsigned long i;

int has_interesting = 0;

for (i = 0; i <= cnt; i++) {

if (interesting(&sline[i], all_mask))

sline[i].flag |= mark;

else

sline[i].flag &= ~mark;

}

if (!dense)

return give_context(sline, cnt, num_parent);

/* Look at each hunk, and if we have changes from only one

* parent, or the changes are the same from all but one

* parent, mark that uninteresting.

*/

i = 0;

while (i <= cnt) {

unsigned long j, hunk_begin, hunk_end;

unsigned long same_diff;

while (i <= cnt && !(sline[i].flag & mark))

i++;

if (cnt < i)

break; /* No more interesting hunks */

hunk_begin = i;

for (j = i + 1; j <= cnt; j++) {

if (!(sline[j].flag & mark)) {

/* Look beyond the end to see if there

* is an interesting line after this

* hunk within context span.

*/

unsigned long la; /* lookahead */

int contin = 0;

la = adjust_hunk_tail(sline, all_mask,

hunk_begin, j);

la = (la + context < cnt + 1) ?

(la + context) : cnt + 1;

while (la && j <= --la) {

if (sline[la].flag & mark) {

contin = 1;

break;

}

}

if (!contin)

break;

j = la;

}

}

hunk_end = j;

/* [i..hunk_end) are interesting. Now is it really

* interesting? We check if there are only two versions

* and the result matches one of them. That is, we look

* at:

* (+) line, which records lines added to which parents;

* this line appears in the result.

* (-) line, which records from what parents the line

* was removed; this line does not appear in the result.

* then check the set of parents the result has difference

* from, from all lines. If there are lines that has

* different set of parents that the result has differences

* from, that means we have more than two versions.

*

* Even when we have only two versions, if the result does

* not match any of the parents, the it should be considered

* interesting. In such a case, we would have all '+' line.

* After passing the above "two versions" test, that would

* appear as "the same set of parents" to be "all parents".

*/

same_diff = 0;

has_interesting = 0;

for (j = i; j < hunk_end && !has_interesting; j++) {

unsigned long this_diff = sline[j].flag & all_mask;

struct lline *ll = sline[j].lost;

if (this_diff) {

/* This has some changes. Is it the

* same as others?

*/

if (!same_diff)

same_diff = this_diff;

else if (same_diff != this_diff) {

has_interesting = 1;

break;

}

}

while (ll && !has_interesting) {

/* Lost this line from these parents;

* who are they? Are they the same?

*/

this_diff = ll->parent_map;

if (!same_diff)

same_diff = this_diff;

else if (same_diff != this_diff) {

has_interesting = 1;

}

ll = ll->next;

}

}

if (!has_interesting && same_diff != all_mask) {

/* This hunk is not that interesting after all */

for (j = hunk_begin; j < hunk_end; j++)

sline[j].flag &= ~mark;

}

i = hunk_end;

}

has_interesting = give_context(sline, cnt, num_parent);

return has_interesting;

}

static void show_parent_lno(struct sline *sline, unsigned long l0, unsigned long l1, int n, unsigned long null_context)

{

l0 = sline[l0].p_lno[n];

l1 = sline[l1].p_lno[n];

printf(" -%lu,%lu", l0, l1-l0-null_context);

}

static int hunk_comment_line(const char *bol)

{

int ch;

if (!bol)

return 0;

ch = *bol & 0xff;

return (isalpha(ch) || ch == '_' || ch == '$');

}

static void show_line_to_eol(const char *line, int len, const char *reset)

{

int saw_cr_at_eol = 0;

if (len < 0)

len = strlen(line);

saw_cr_at_eol = (len && line[len-1] == '\r');

printf("%.*s%s%s\n", len - saw_cr_at_eol, line,

reset,

saw_cr_at_eol ? "\r" : "");

}

static void dump_sline(struct sline *sline, const char *line_prefix,

unsigned long cnt, int num_parent,

int use_color, int result_deleted)

{

unsigned long mark = (1UL<

unsigned long no_pre_delete = (2UL<

int i;

unsigned long lno = 0;

const char *c_frag = diff_get_color(use_color, DIFF_FRAGINFO);

const char *c_func = diff_get_color(use_color, DIFF_FUNCINFO);

const char *c_new = diff_get_color(use_color, DIFF_FILE_NEW);

const char *c_old = diff_get_color(use_color, DIFF_FILE_OLD);

const char *c_context = diff_get_color(use_color, DIFF_CONTEXT);

const char *c_reset = diff_get_color(use_color, DIFF_RESET);

if (result_deleted)

return; /* result deleted */

while (1) {

unsigned long hunk_end;

unsigned long rlines;

const char *hunk_comment = NULL;

unsigned long null_context = 0;

while (lno <= cnt && !(sline[lno].flag & mark)) {

if (hunk_comment_line(sline[lno].bol))

hunk_comment = sline[lno].bol;

lno++;

}

if (cnt < lno)

break;

else {

for (hunk_end = lno + 1; hunk_end <= cnt; hunk_end++)

if (!(sline[hunk_end].flag & mark))

break;

}

rlines = hunk_end - lno;

if (cnt < hunk_end)

rlines--; /* pointing at the last delete hunk */

if (!context) {

/*

* Even when running with --unified=0, all

* lines in the hunk needs to be processed in

* the loop below in order to show the

* deletion recorded in lost_head. However,

* we do not want to show the resulting line

* with all blank context markers in such a

* case. Compensate.

*/

unsigned long j;

for (j = lno; j < hunk_end; j++)

if (!(sline[j].flag & (mark-1)))

null_context++;

rlines -= null_context;

}

printf("%s%s", line_prefix, c_frag);

for (i = 0; i <= num_parent; i++) putchar(combine_marker);

for (i = 0; i < num_parent; i++)

show_parent_lno(sline, lno, hunk_end, i, null_context);

printf(" +%lu,%lu ", lno+1, rlines);

for (i = 0; i <= num_parent; i++) putchar(combine_marker);

if (hunk_comment) {

int comment_end = 0;

for (i = 0; i < 40; i++) {

int ch = hunk_comment[i] & 0xff;

if (!ch || ch == '\n')

break;

if (!isspace(ch))

comment_end = i;

}

if (comment_end)

printf("%s%s %s%s", c_reset,

c_context, c_reset,

c_func);

for (i = 0; i < comment_end; i++)

putchar(hunk_comment[i]);

}

printf("%s\n", c_reset);

while (lno < hunk_end) {

struct lline *ll;

int j;

unsigned long p_mask;

struct sline *sl = &sline[lno++];

ll = (sl->flag & no_pre_delete) ? NULL : sl->lost;

while (ll) {

printf("%s%s", line_prefix, c_old);

for (j = 0; j < num_parent; j++) {

if (ll->parent_map & (1UL<

putchar('-');

else

putchar(' ');

}

show_line_to_eol(ll->line, -1, c_reset);

ll = ll->next;

}

if (cnt < lno)

break;

p_mask = 1;

fputs(line_prefix, stdout);

if (!(sl->flag & (mark-1))) {

/*

* This sline was here to hang the

* lost lines in front of it.

*/

if (!context)

continue;

fputs(c_context, stdout);

}

else

fputs(c_new, stdout);

for (j = 0; j < num_parent; j++) {

if (p_mask & sl->flag)

putchar('+');

else

putchar(' ');

p_mask <<= 1;

}

show_line_to_eol(sl->bol, sl->len, c_reset);

}

}

}

static void reuse_combine_diff(struct sline *sline, unsigned long cnt,

int i, int j)

{

/* We have already examined parent j and we know parent i

* and parent j are the same, so reuse the combined result

* of parent j for parent i.

*/

unsigned long lno, imask, jmask;

imask = (1UL<

jmask = (1UL<

for (lno = 0; lno <= cnt; lno++) {

struct lline *ll = sline->lost;

sline->p_lno[i] = sline->p_lno[j];

while (ll) {

if (ll->parent_map & jmask)

ll->parent_map |= imask;

ll = ll->next;

}

if (sline->flag & jmask)

sline->flag |= imask;

sline++;

}

/* the overall size of the file (sline[cnt]) */

sline->p_lno[i] = sline->p_lno[j];

}

static void dump_quoted_path(const char *head,

const char *prefix,

const char *path,

const char *line_prefix,

const char *c_meta, const char *c_reset)

{

static struct strbuf buf = STRBUF_INIT;

strbuf_reset(&buf);

strbuf_addstr(&buf, line_prefix);

strbuf_addstr(&buf, c_meta);

strbuf_addstr(&buf, head);

quote_two_c_style(&buf, prefix, path, 0);

strbuf_addstr(&buf, c_reset);

puts(buf.buf);

}

static void show_combined_header(struct combine_diff_path *elem,

int num_parent,

int dense,

struct rev_info *rev,

const char *line_prefix,

int mode_differs,

int show_file_header)

{

struct diff_options *opt = &rev->diffopt;

int abbrev = opt->flags.full_index ? the_hash_algo->hexsz : DEFAULT_ABBREV;

const char *a_prefix = opt->a_prefix ? opt->a_prefix : "a/";

const char *b_prefix = opt->b_prefix ? opt->b_prefix : "b/";

const char *c_meta = diff_get_color_opt(opt, DIFF_METAINFO);

const char *c_reset = diff_get_color_opt(opt, DIFF_RESET);

const char *abb;

int added = 0;

int deleted = 0;

int i;

if (rev->loginfo && !rev->no_commit_id)

show_log(rev);

dump_quoted_path(dense ? "diff --cc " : "diff --combined ",

"", elem->path, line_prefix, c_meta, c_reset);

printf("%s%sindex ", line_prefix, c_meta);

for (i = 0; i < num_parent; i++) {

abb = find_unique_abbrev(&elem->parent[i].oid,

abbrev);

printf("%s%s", i ? "," : "", abb);

}

abb = find_unique_abbrev(&elem->oid, abbrev);

printf("..%s%s\n", abb, c_reset);

if (mode_differs) {

deleted = !elem->mode;

/* We say it was added if nobody had it */

added = !deleted;

for (i = 0; added && i < num_parent; i++)

if (elem->parent[i].status !=

DIFF_STATUS_ADDED)

added = 0;

if (added)

printf("%s%snew file mode %06o",

line_prefix, c_meta, elem->mode);

else {

if (deleted)

printf("%s%sdeleted file ",

line_prefix, c_meta);

printf("mode ");

for (i = 0; i < num_parent; i++) {

printf("%s%06o", i ? "," : "",

elem->parent[i].mode);

}

if (elem->mode)

printf("..%06o", elem->mode);

}

printf("%s\n", c_reset);

}

if (!show_file_header)

return;

if (rev->combined_all_paths) {

for (i = 0; i < num_parent; i++) {

char *path = filename_changed(elem->parent[i].status)

? elem->parent[i].path.buf : elem->path;

if (elem->parent[i].status == DIFF_STATUS_ADDED)

dump_quoted_path("--- ", "", "/dev/null",

line_prefix, c_meta, c_reset);

else

dump_quoted_path("--- ", a_prefix, path,

line_prefix, c_meta, c_reset);

}

} else {

if (added)

dump_quoted_path("--- ", "", "/dev/null",

line_prefix, c_meta, c_reset);

else

dump_quoted_path("--- ", a_prefix, elem->path,

line_prefix, c_meta, c_reset);

}

if (deleted)

dump_quoted_path("+++ ", "", "/dev/null",

line_prefix, c_meta, c_reset);

else

dump_quoted_path("+++ ", b_prefix, elem->path,

line_prefix, c_meta, c_reset);

}

static void show_patch_diff(struct combine_diff_path *elem, int num_parent,

int dense, int working_tree_file,

struct rev_info *rev)

{

struct diff_options *opt = &rev->diffopt;

unsigned long result_size, cnt, lno;

int result_deleted = 0;

char *result, *cp;

struct sline *sline; /* survived lines */

int mode_differs = 0;

int i, show_hunks;

mmfile_t result_file;

struct userdiff_driver *userdiff;

struct userdiff_driver *textconv = NULL;

int is_binary;

const char *line_prefix = diff_line_prefix(opt);

context = opt->context;

userdiff = userdiff_find_by_path(opt->repo->index, elem->path);

if (!userdiff)

userdiff = userdiff_find_by_name("default");

if (opt->flags.allow_textconv)

textconv = userdiff_get_textconv(opt->repo, userdiff);

/* Read the result of merge first */

if (!working_tree_file)

result = grab_blob(opt->repo, &elem->oid, elem->mode, &result_size,

textconv, elem->path);

else {

/* Used by diff-tree to read from the working tree */

struct stat st;

int fd = -1;

if (lstat(elem->path, &st) < 0)

goto deleted_file;

if (S_ISLNK(st.st_mode)) {

struct strbuf buf = STRBUF_INIT;

if (strbuf_readlink(&buf, elem->path, st.st_size) < 0) {

error_errno("readlink(%s)", elem->path);

return;

}

result_size = buf.len;

result = strbuf_detach(&buf, NULL);

elem->mode = canon_mode(st.st_mode);

} else if (S_ISDIR(st.st_mode)) {

struct object_id oid;

if (resolve_gitlink_ref(elem->path, "HEAD", &oid) < 0)

result = grab_blob(opt->repo, &elem->oid,

elem->mode, &result_size,

NULL, NULL);

else

result = grab_blob(opt->repo, &oid, elem->mode,

&result_size, NULL, NULL);

} else if (textconv) {

struct diff_filespec *df = alloc_filespec(elem->path);

fill_filespec(df, &null_oid, 0, st.st_mode);

result_size = fill_textconv(opt->repo, textconv, df, &result);

free_filespec(df);

} else if (0 <= (fd = open(elem->path, O_RDONLY))) {

size_t len = xsize_t(st.st_size);

ssize_t done;

int is_file, i;

elem->mode = canon_mode(st.st_mode);

/* if symlinks don't work, assume symlink if all parents

* are symlinks

*/

is_file = has_symlinks;

for (i = 0; !is_file && i < num_parent; i++)

is_file = !S_ISLNK(elem->parent[i].mode);

if (!is_file)

elem->mode = canon_mode(S_IFLNK);

result_size = len;

result = xmallocz(len);

done = read_in_full(fd, result, len);

if (done < 0)

die_errno("read error '%s'", elem->path);

else if (done < len)

die("early EOF '%s'", elem->path);

/* If not a fake symlink, apply filters, e.g. autocrlf */

if (is_file) {

struct strbuf buf = STRBUF_INIT;

if (convert_to_git(rev->diffopt.repo->index,

elem->path, result, len, &buf, global_conv_flags_eol)) {

free(result);

result = strbuf_detach(&buf, &len);

result_size = len;

}

}

}

else {

deleted_file:

result_deleted = 1;

result_size = 0;

elem->mode = 0;

result = xcalloc(1, 1);

}

if (0 <= fd)

close(fd);

}

for (i = 0; i < num_parent; i++) {

if (elem->parent[i].mode != elem->mode) {

mode_differs = 1;

break;

}

}

if (textconv)

is_binary = 0;

else if (userdiff->binary != -1)

is_binary = userdiff->binary;

else {

is_binary = buffer_is_binary(result, result_size);

for (i = 0; !is_binary && i < num_parent; i++) {

char *buf;

unsigned long size;

buf = grab_blob(opt->repo,

&elem->parent[i].oid,

elem->parent[i].mode,

&size, NULL, NULL);

if (buffer_is_binary(buf, size))

is_binary = 1;

free(buf);

}

}

if (is_binary) {

show_combined_header(elem, num_parent, dense, rev,

line_prefix, mode_differs, 0);

printf("Binary files differ\n");

free(result);

return;

}

for (cnt = 0, cp = result; cp < result + result_size; cp++) {

if (*cp == '\n')

cnt++;

}

if (result_size && result[result_size-1] != '\n')

cnt++; /* incomplete line */

sline = xcalloc(st_add(cnt, 2), sizeof(*sline));

sline[0].bol = result;

for (lno = 0, cp = result; cp < result + result_size; cp++) {

if (*cp == '\n') {

sline[lno].len = cp - sline[lno].bol;

lno++;

if (lno < cnt)

sline[lno].bol = cp + 1;

}

}

if (result_size && result[result_size-1] != '\n')

sline[cnt-1].len = result_size - (sline[cnt-1].bol - result);

result_file.ptr = result;

result_file.size = result_size;

/* Even p_lno[cnt+1] is valid -- that is for the end line number

* for deletion hunk at the end.

*/

sline[0].p_lno = xcalloc(st_mult(st_add(cnt, 2), num_parent), sizeof(unsigned long));

for (lno = 0; lno <= cnt; lno++)

sline[lno+1].p_lno = sline[lno].p_lno + num_parent;

for (i = 0; i < num_parent; i++) {

int j;

for (j = 0; j < i; j++) {

if (oideq(&elem->parent[i].oid,

&elem->parent[j].oid)) {

reuse_combine_diff(sline, cnt, i, j);

break;

}

}

if (i <= j)

combine_diff(opt->repo,

&elem->parent[i].oid,

elem->parent[i].mode,

&result_file, sline,

cnt, i, num_parent, result_deleted,

textconv, elem->path, opt->xdl_opts);

}

show_hunks = make_hunks(sline, cnt, num_parent, dense);

if (show_hunks || mode_differs || working_tree_file) {

show_combined_header(elem, num_parent, dense, rev,

line_prefix, mode_differs, 1);

dump_sline(sline, line_prefix, cnt, num_parent,

opt->use_color, result_deleted);

}

free(result);

for (lno = 0; lno < cnt; lno++) {

if (sline[lno].lost) {

struct lline *ll = sline[lno].lost;

while (ll) {

struct lline *tmp = ll;

ll = ll->next;

free(tmp);

}

}

}

free(sline[0].p_lno);

free(sline);

}

static void show_raw_diff(struct combine_diff_path *p, int num_parent, struct rev_info *rev)

{

struct diff_options *opt = &rev->diffopt;

int line_termination, inter_name_termination, i;

const char *line_prefix = diff_line_prefix(opt);

line_termination = opt->line_termination;

inter_name_termination = '\t';

if (!line_termination)

inter_name_termination = 0;

if (rev->loginfo && !rev->no_commit_id)

show_log(rev);

if (opt->output_format & DIFF_FORMAT_RAW) {

printf("%s", line_prefix);

/* As many colons as there are parents */

for (i = 0; i < num_parent; i++)

putchar(':');

/* Show the modes */

for (i = 0; i < num_parent; i++)

printf("%06o ", p->parent[i].mode);

printf("%06o", p->mode);

/* Show sha1's */

for (i = 0; i < num_parent; i++)

printf(" %s", diff_aligned_abbrev(&p->parent[i].oid,

opt->abbrev));

printf(" %s ", diff_aligned_abbrev(&p->oid, opt->abbrev));

}

if (opt->output_format & (DIFF_FORMAT_RAW | DIFF_FORMAT_NAME_STATUS)) {

for (i = 0; i < num_parent; i++)

putchar(p->parent[i].status);

putchar(inter_name_termination);

}

for (i = 0; i < num_parent; i++)

if (rev->combined_all_paths) {

if (filename_changed(p->parent[i].status))

write_name_quoted(p->parent[i].path.buf, stdout,

inter_name_termination);

else

write_name_quoted(p->path, stdout,

inter_name_termination);

}

write_name_quoted(p->path, stdout, line_termination);

}

/*

* The result (p->elem) is from the working tree and their

* parents are typically from multiple stages during a merge

* (i.e. diff-files) or the state in HEAD and in the index

* (i.e. diff-index).

*/

void show_combined_diff(struct combine_diff_path *p,

int num_parent,

int dense,

struct rev_info *rev)

{

struct diff_options *opt = &rev->diffopt;

if (opt->output_format & (DIFF_FORMAT_RAW |

DIFF_FORMAT_NAME |

DIFF_FORMAT_NAME_STATUS))

show_raw_diff(p, num_parent, rev);

else if (opt->output_format & DIFF_FORMAT_PATCH)

show_patch_diff(p, num_parent, dense, 1, rev);

}

static void free_combined_pair(struct diff_filepair *pair)

{

free(pair->two);

free(pair);

}

/*

* A combine_diff_path expresses N parents on the LHS against 1 merge

* result. Synthesize a diff_filepair that has N entries on the "one"

* side and 1 entry on the "two" side.

*

* In the future, we might want to add more data to combine_diff_path

* so that we can fill fields we are ignoring (most notably, size) here,

* but currently nobody uses it, so this should suffice for now.

*/

static struct diff_filepair *combined_pair(struct combine_diff_path *p,

int num_parent)

{

int i;

struct diff_filepair *pair;

struct diff_filespec *pool;

pair = xmalloc(sizeof(*pair));

pool = xcalloc(st_add(num_parent, 1), sizeof(struct diff_filespec));

pair->one = pool + 1;

pair->two = pool;

for (i = 0; i < num_parent; i++) {

pair->one[i].path = p->path;

pair->one[i].mode = p->parent[i].mode;

oidcpy(&pair->one[i].oid, &p->parent[i].oid);

pair->one[i].oid_valid = !is_null_oid(&p->parent[i].oid);

pair->one[i].has_more_entries = 1;

}

pair->one[num_parent - 1].has_more_entries = 0;

pair->two->path = p->path;

pair->two->mode = p->mode;

oidcpy(&pair->two->oid, &p->oid);

pair->two->oid_valid = !is_null_oid(&p->oid);

return pair;

}

static void handle_combined_callback(struct diff_options *opt,

struct combine_diff_path *paths,

int num_parent,

int num_paths)

{

struct combine_diff_path *p;

struct diff_queue_struct q;

int i;

q.queue = xcalloc(num_paths, sizeof(struct diff_filepair *));

q.alloc = num_paths;

q.nr = num_paths;

for (i = 0, p = paths; p; p = p->next)

q.queue[i++] = combined_pair(p, num_parent);

opt->format_callback(&q, opt, opt->format_callback_data);

for (i = 0; i < num_paths; i++)

free_combined_pair(q.queue[i]);

free(q.queue);

}

static const char *path_path(void *obj)

{

struct combine_diff_path *path = (struct combine_diff_path *)obj;

return path->path;

}

/*

* Diff stat formats which we always compute solely against the first parent.

*/

#define STAT_FORMAT_MASK (DIFF_FORMAT_NUMSTAT \

| DIFF_FORMAT_SHORTSTAT \

| DIFF_FORMAT_SUMMARY \

| DIFF_FORMAT_DIRSTAT \

| DIFF_FORMAT_DIFFSTAT)

/* find set of paths that every parent touches */

static struct combine_diff_path *find_paths_generic(const struct object_id *oid,

const struct oid_array *parents,

struct diff_options *opt,

int combined_all_paths)

{

struct combine_diff_path *paths = NULL;

int i, num_parent = parents->nr;

int output_format = opt->output_format;

const char *orderfile = opt->orderfile;

opt->output_format = DIFF_FORMAT_NO_OUTPUT;

/* tell diff_tree to emit paths in sorted (=tree) order */

opt->orderfile = NULL;

/* D(A,P1...Pn) = D(A,P1) ^ ... ^ D(A,Pn) (wrt paths) */

for (i = 0; i < num_parent; i++) {

/*

* show stat against the first parent even when doing

* combined diff.

*/

int stat_opt = output_format & STAT_FORMAT_MASK;

if (i == 0 && stat_opt)

opt->output_format = stat_opt;

else

opt->output_format = DIFF_FORMAT_NO_OUTPUT;

diff_tree_oid(&parents->oid[i], oid, "", opt);

diffcore_std(opt);

paths = intersect_paths(paths, i, num_parent,

combined_all_paths);

/* if showing diff, show it in requested order */

if (opt->output_format != DIFF_FORMAT_NO_OUTPUT &&

orderfile) {

diffcore_order(orderfile);

}

diff_flush(opt);

}

opt->output_format = output_format;

opt->orderfile = orderfile;

return paths;

}

/*

* find set of paths that everybody touches, assuming diff is run without

* rename/copy detection, etc, comparing all trees simultaneously (= faster).

*/

static struct combine_diff_path *find_paths_multitree(

const struct object_id *oid, const struct oid_array *parents,

struct diff_options *opt)

{

int i, nparent = parents->nr;

const struct object_id **parents_oid;

struct combine_diff_path paths_head;

struct strbuf base;

ALLOC_ARRAY(parents_oid, nparent);

for (i = 0; i < nparent; i++)

parents_oid[i] = &parents->oid[i];

/* fake list head, so worker can assume it is non-NULL */

paths_head.next = NULL;

strbuf_init(&base, PATH_MAX);

diff_tree_paths(&paths_head, oid, parents_oid, nparent, &base, opt);

strbuf_release(&base);

free(parents_oid);

return paths_head.next;

}

void diff_tree_combined(const struct object_id *oid,

const struct oid_array *parents,

int dense,

struct rev_info *rev)

{

struct diff_options *opt = &rev->diffopt;

struct diff_options diffopts;

struct combine_diff_path *p, *paths;

int i, num_paths, needsep, show_log_first, num_parent = parents->nr;

int need_generic_pathscan;

/* nothing to do, if no parents */

if (!num_parent)

return;

show_log_first = !!rev->loginfo && !rev->no_commit_id;

needsep = 0;

if (show_log_first) {

show_log(rev);

if (rev->verbose_header && opt->output_format &&

opt->output_format != DIFF_FORMAT_NO_OUTPUT &&

!commit_format_is_empty(rev->commit_format))

printf("%s%c", diff_line_prefix(opt),

opt->line_termination);

}

diffopts = *opt;

copy_pathspec(&diffopts.pathspec, &opt->pathspec);

diffopts.flags.recursive = 1;

diffopts.flags.allow_external = 0;

/* find set of paths that everybody touches

*

* NOTE

*

* Diffcore transformations are bound to diff_filespec and logic

* comparing two entries - i.e. they do not apply directly to combine

* diff.

*

* If some of such transformations is requested - we launch generic

* path scanning, which works significantly slower compared to

* simultaneous all-trees-in-one-go scan in find_paths_multitree().

*

* TODO some of the filters could be ported to work on

* combine_diff_paths - i.e. all functionality that skips paths, so in

* theory, we could end up having only multitree path scanning.

*

* NOTE please keep this semantically in sync with diffcore_std()

*/

need_generic_pathscan = opt->skip_stat_unmatch||

opt->flags.follow_renames||

opt->break_opt != -1||

opt->detect_rename||

(opt->pickaxe_opts & DIFF_PICKAXE_KINDS_MASK)||

opt->filter;

if (need_generic_pathscan) {

/*

* NOTE generic case also handles --stat, as it computes

* diff(sha1,parent_i) for all i to do the job, specifically

* for parent0.

*/

paths = find_paths_generic(oid, parents, &diffopts,

rev->combined_all_paths);

}

else {

int stat_opt;

paths = find_paths_multitree(oid, parents, &diffopts);

/*

* show stat against the first parent even

* when doing combined diff.

*/

stat_opt = opt->output_format & STAT_FORMAT_MASK;

if (stat_opt) {

diffopts.output_format = stat_opt;

diff_tree_oid(&parents->oid[0], oid, "", &diffopts);

diffcore_std(&diffopts);

if (opt->orderfile)

diffcore_order(opt->orderfile);

diff_flush(&diffopts);

}

}

/* find out number of surviving paths */

for (num_paths = 0, p = paths; p; p = p->next)

num_paths++;

/* order paths according to diffcore_order */

if (opt->orderfile && num_paths) {

struct obj_order *o;

ALLOC_ARRAY(o, num_paths);

for (i = 0, p = paths; p; p = p->next, i++)

o[i].obj = p;

order_objects(opt->orderfile, path_path, o, num_paths);

for (i = 0; i < num_paths - 1; i++) {

p = o[i].obj;

p->next = o[i+1].obj;

}

p = o[num_paths-1].obj;

p->next = NULL;

paths = o[0].obj;

free(o);

}

if (num_paths) {

if (opt->output_format & (DIFF_FORMAT_RAW |

DIFF_FORMAT_NAME |

DIFF_FORMAT_NAME_STATUS)) {

for (p = paths; p; p = p->next)

show_raw_diff(p, num_parent, rev);

needsep = 1;

}

else if (opt->output_format & STAT_FORMAT_MASK)

needsep = 1;

else if (opt->output_format & DIFF_FORMAT_CALLBACK)

handle_combined_callback(opt, paths, num_parent, num_paths);

if (opt->output_format & DIFF_FORMAT_PATCH) {

if (needsep)

printf("%s%c", diff_line_prefix(opt),

opt->line_termination);

for (p = paths; p; p = p->next)

show_patch_diff(p, num_parent, dense,

0, rev);

}

}

/* Clean things up */

while (paths) {

struct combine_diff_path *tmp = paths;

paths = paths->next;

for (i = 0; i < num_parent; i++)

if (rev->combined_all_paths &&

filename_changed(tmp->parent[i].status))

strbuf_release(&tmp->parent[i].path);

free(tmp);

}

clear_pathspec(&diffopts.pathspec);

}

void diff_tree_combined_merge(const struct commit *commit, int dense,

struct rev_info *rev)

{

struct commit_list *parent = get_saved_parents(rev, commit);

struct oid_array parents = OID_ARRAY_INIT;

while (parent) {

oid_array_append(&parents, &parent->item->object.oid);

parent = parent->next;

}

diff_tree_combined(&commit->object.oid, &parents, dense, rev);

oid_array_clear(&parents);

}

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使用GATK的combinegvcf模块合并gvcf文件,可是到了这一步Using GATK jar /stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar CombineGVCFs -R /stor9000/apps/users/NWSUAF/2008115251/genomes/ARS-UCD1.2_Btau5.0.1Y.fa --variant /stor9000/apps/users/NWSUAF/2020055419/home/xncattle/03.GVCF/01_out_GVCF/XN_22/1_XN_22.g.vcf.gz --variant /stor9000/apps/users/NWSUAF/2020055419/home/xncattle/03.GVCF/01_out_GVCF/XN_18/1_XN_18.g.vcf.gz -O /stor9000/apps/users/NWSUAF/2022050469/candy/bwa/gatk/Combine/chr1.g.vcf.gz 09:10:40.524 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 09:10:50.696 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.697 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.3.0.0 09:10:50.697 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:10:50.698 INFO CombineGVCFs - Executing as 2022050469@node54 on Linux v3.10.0-1127.el7.x86_64 amd64 09:10:50.698 INFO CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_72-b15 09:10:50.698 INFO CombineGVCFs - Start Date/Time: July 21, 2023 9:10:40 AM CST 09:10:50.698 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.698 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.698 INFO CombineGVCFs - HTSJDK Version: 3.0.1 09:10:50.699 INFO CombineGVCFs - Picard Version: 2.27.5 09:10:50.699 INFO CombineGVCFs - Built for Spark Version: 2.4.5 09:10:50.699 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:10:50.699 INFO CombineGVCFs - HTSJDK Defa就停止了,没有输出文件,也没有报错文件
07-22
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